http://www.proginosko.com/docs/wcf_lbcf.html#WCF20
WCF Chap 20 Section 2 says "God alone is Lord of the conscience, and hath left it free from the doctrines and commandments of men which are in any thing contrary to his word, or beside it in matters of faith or worship. So that to believe such doctrines, or to obey such commandments out of conscience, is to betray true liberty of conscience; and the requiring of an implicit faith, and an absolute and blind obedience, is to destroy liberty of conscience, and reason also." This is often appealed to. Yet the Confession distinguishes between true liberty of conscience and pretended liberty of conscience. The latter seeks a liberty of conscience beyond the bounds of Scripture and which cannot be restrained by any lawful authority. Section 4 of chapter 20 deals with these biblical limits. This is the section removed by the London Baptist Confession. The appeal to liberty of conscience is not an uncomplicated one and does not automatically mean that Church courts do not have the right to restrain conscience in some ways.
How conscience may be compelled
George Gillespie stated: "If the thing be indifferent, I confess no man is to be compelled to it against his conscience, for this hath been the tyranny of Papists and Prelates, to compel men against their consciences to certain rites which themselves acknowledge to be merely indifferent, setting aside obedience to authority in such things, which (they say) is not indifferent. But if the word of God either directly or by necessary consequence, make the thing necessary, and such as we cannot leave undone without sin and breach of duty; if there be such an obligation from the word, then may a man be compelled to it, though against his conscience." (Wholesome Severity reconciled with Christian Liberty). This is the balance of the Confession - that there is liberty of conscience and yet a man may be compelled against his conscience by the powers which God has ordained. In Section 4 of chapter 20 the Confession goes on to qualify and limit what it says on liberty of conscience: "And because the powers which God hath ordained, and the liberty which Christ hath purchased, are not intended by God to destroy, but mutually to uphold and preserve one another, they who, upon pretense of Christian liberty, shall oppose any lawful power, or the lawful exercise of it, whether it be civil or ecclesiastical, resist the ordinance of God. And, for their publishing of such opinions, or maintaining of such practices, as are contrary to the light of nature, or to the known principles of Christianity (whether concerning faith, worship, or conversation), or to the power of godliness; or, such erroneous opinions or practices, as either in their own nature, or in the manner of publishing or maintaining them, are destructive to the external peace and order which Christ hath established in the church, they may lawfully be called to account, and proceeded against, by the censures of the church."
Dr M'Crie notes that: "The design of section fourth is to guard against the abuse of the doctrine of liberty of conscience in reference to public authority. 'And because the powers which God hath ordained, and the liberty which Christ hath purchased, are not intended by God to destroy, but mutually to uphold and preserve one another, they who, upon pretence of Christian liberty, shall oppose any lawful power, or the lawful exercise of it, whether it be civil or ecclesiastical, resist the ordinance of God.' He who is the Lord of the conscience has also instituted the authorities in Church and State; and it would be in the highest degree absurd to suppose that he has planted in the breast of every individual a power to resist, counteract, and nullify his own ordinances. When public and private claims interfere and clash, the latter must give way to the former; and when any lawful authority is proceeding lawfully within its line of duty, it must be understood as possessing a rightful power to remove out of the way everything which necessarily obstructs its progress. The Confession proceeds, accordingly, to state: 'And for their publishing of such opinions, or maintaining of such practices, as are contrary to the light of nature; or to the known principles of Christianity whether concerning faith, worship, or conversation, or to the power of godliness; or such erroneous opinions or practices as, either in their own nature or in the manner of publishing and maintaining them, are destructive to the external peace and order which Christ hath established in the Church; they may lawfully be called to account, and proceeded against by the censures of the Church, and by the power of the civil magistrate.' Individual liberty is regulated by the principles found in Scripture and is limited by the mutual duties believers owe to one another, and by concern for the welfare of all men.
Conscience - internal and external aspects
We must draw a distinction between conscience in its internal and external aspects. Alternatively we may speak of conscience in its invisible aspect (a man's mind, his thoughts and beliefs) and in its visible aspect (when these beliefs opinions are expressed publicly either verbally or through action). This is in relation to the authority of both Church and State. "We say the magistrate or his sword hath nothing to do with the elect and internal acts of the mind, of understanding, knowing, judging or believing, but only with the external acts of speaking, teaching, publishing dangerous and pernicious doctrines to the hurt and destruction of the souls of others" (Rutherford, A Free Disputation, p.62). No magistrate can coerce or force someone to believe something; they can only prevent them from promoting such opinions as are contrary to the truth by preaching, printing, spreading of dangerous opinions, schismatic, pernicious, and scandalous practices, or drawing factions among the people.
The same principle obtains for Church courts."...it is certain that human laws, as they come from men, and in respect of any force or authority which men can give them, have no power to bind the conscience. For the business of our consciences is not with men, but with the one God, says Calvin. [Instit. lib. 4, cap. 10, sect. 5.] Over our souls and consciences, no one except God has any right, says Tilen. [Synt., part. 2, disp. 32, thes. 4.] From Jerome's distinction, that a king is in charge of the unwilling, but a bishop the willing, Marcus Antonius de Dominis well concludes: to be in charge of the willing as a flock removes all legal authority and power to command and force, and signifies only power to guide where, viz., the subject is at liberty to comply and not to comply, such that the one who is in charge has nothing by which to compel to compliance one who does not want to comply. [De Rep. Eccl., lib. 5, cap. 2, n. 12.] This point he proves in that chapter at length, where he disputes both against temporal and spiritual coactive jurisdiction in the church." Gillespie, A Dispute Against the English Popish Ceremonies (Naphtali Press, 1993) I-4-3. pp. 12-13. Again Gillespie asserts the distinction between private opinions in the mind and public practices based on them. "I distinguish betwixt bare opinions or speculations, and scandalous or pernicious practices, as Mr. Burton doth in his Vindication of the Independent Churches, page 70. You must distinguish, saith he, betwixt mens consciences and their practices. The conscience simply considered in itself is for God the Lord of the conscience alone to judge, as before. But for a man's practices (of which alone man can take cognizance) if they be against any of God's commandments of the first or second Table; that appertains to the civil Magistrate to punish, who is for this cause called Custos utriusque Tabulæ, the keeper of both Tables: for this he citeth Rom. 13.3,4, and addeth: So as we see here what is the object of civil power, to wit, actions good or bad, not bare opinions, not thoughts, not conscience, but actions." (Wholesome Severity reconciled with Christian Liberty).
The Reformers also made this distinction, Heinrich Bullinger said "...while false faith doth lurk and lie hid within the heart, and infecteth none but the unbeliever, so long the unbelieving infidel cannot be punished: but if this false and forged faith, that so lay hid, do once break forth to blaspheme, to the open tearing of God and the infecting of his neighbours, then must that blasphemer and seducer be by and by plucked under, and kept from creeping to further annoyance."(Decade 2, Sermon 8, p. 363 in Parker Society edition).
What we are establishing is that the distinction between internal and external acts of conscience enunciated by those who framed the Westminster Confession (viz. Rutherford and Gillespie) is encapsulated in the Confession itself in 20:4. The powers ordained by God have authority to restrain the public acts of conscience in this way. So Rutherford says "Christ hath left the consciences of false teachers and heretics under ecclesiastical censures of admonitions, rebukes, excommunication" (A Free Disputation, p.235). Thus the appeal to liberty of conscience is not an uncomplicated one and does not automatically mean that Church courts do not have the right to restrain conscience in some ways. While Church courts cannot impose aspects of faith and worship by their sole authority they can apply that which is in God's Word. "The dogmatic power of a synod is not a power to make new articles of faith, nor new duties and parts of divine worship, but a power to apply and interpret those articles of faith and duties of worship which God hath set before us in his written word, and to declare the same to be inconsistent with emergent heresies and errors." Notice that Gillespie highlights what the WCF highlights in 20:2, that our consciences are left free from "the doctrines and commandments of men which are in any thing contrary to his word, or beside it in matters of faith or worship" (my italics). To compel a man to believe something by force is persecution but to compel a man to desist from creating division, disorder, damage stemming from erroneous views and opinions and through expressing or acting upon them publicly is within the lawful powers of the Church and State. The Westminster divines were well aware of what persecution was from the Laudian inquisition of the 1630's which sought to punish men for their beliefs whether expressed or not.
An objection to this which Gillespie acknowledges is someone who may say when compelled to obey "I am brought into a necessity of sinning, for if I obey not, I refuse a duty; if I obey, I do it against my conscience. Answer. This necessity is not absolute, but hypothetical, is not per se, but per accidens, so long as a man retaineth the error of his conscience, which he ought to cast away. You will say again, supposing that my conscience cannot be satisfied, nor made of another opinion than now I am of, whether in this case, and so long as it standeth thus with me, may authority compel me to obey against my conscience, and so to sin? or whether ought they not rather permit me not to obey, because my conscience forbiddeth me. Answer. The thing being necessary, as hath been said, it is pars tutior, yea, tutissima, that a man be compelled to it, though it be against his erring and ill informed conscience. I know so long as he hath such an erring conscience he cannot but sin in obeying. But the sin of not obeying is greater and heavier: for this is a sin in the fact itself; that a sin in the manner of doing only, being not done in faith: this is a sin of itself; that is a sin only by accident: this is a sin materially; that is a sin only interpretatively to him, because he thinks so: this is a sin for the substance; that a sin for the circumstance: this cannot be made to be no sin, for the nature of the duty cannot be altered; that may cease to be a sin, for the man's conscience may through God's mercy and blessing upon the means, be better informed. So that there can be no doubt but this is every way a greater sin than that, and consequently more to be avoided." (Wholesome Severity)
Liberty of conscience is not the same thing as the right of free speech, the Confession does not uphold the unlimited right of free speech. Its position preserves the right of private judgement and rejects persecution, but it is against the very God-given role of the Church and State to permit heresy and division to burn uncontrollably. This is the sense of Act II 1846 which declared the interpretation of the Confession at this point. The Church did not regard her Confession "as favouring intolerance or persecuting principles", nor did she consider "that her office-bearers, by subscribing it, profess any principles inconsistent with liberty of conscience and the right of private judgement". Hence also The Practice of the Free Church of Scotland (and the Free Presbyterian Church of Scotland Manual of Practice), says: "That the Free Church maintains more emphatically that no authority in the hands of fallible men, such as the authority of the General Assembly, has any absolute rule over the consciences of believers, and that every one of her members may appeal to the Great Head of the Church against any such merely ministerial authority" (i.e. dissent with reasons) Chapter 4 Part 2.
Within the context of a Church court therefore, liberty of conscience is fully preserved when dissent is registered. The conscience is not compelled internally but able to be cleared. By dissenting with reasons a man keeps his conscience clear from the responsibility of what he does not approve of. He has no responsibility for the steps leading up to and the passing of a decision but not of obedience to it. Dissent is merely an expression of disagreement not of non-compliance. Non-compliance means resistance and disobedience. As the American Schism of 1741 highlighted, the issue is that of whether church courts have the authority and right to bind the consciences of dissenting members.
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