Chapter XX. Of Christian Liberty, and Liberty of Conscience

IV. 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 be lawfully called to account, and proceeded against by the censures of the Church, and by the power of the civil magistrate.

What changed, and when. The words in bold were struck out in 1788, at the Synod of New York and Philadelphia. The rest of the paragraph remained the same: he who disturbs the peace of the church with his opinions answers to the church, but no longer to the magistrate.

Why. It was not a last-minute novelty. As early as 1729, on adopting the Confession, the Presbyterians of the colonies had taken express exception to this clause, denying the magistrate the "power to persecute any for their Religion". Several things had their influence:
1) Experience: in Scotland and in Ireland they had themselves suffered the intrusion of the civil power into the church (patronage, imposed oaths), and in the colonies they were, in many places, dissenters over against an established church.
2) The situation: in the new republic no church could aspire to be the established one, and the established churches inherited from the colonial period were falling (Virginia passed its statute for religious freedom in 1786).
3) Ideas, and this is the decisive point. Experience and situation help to understand the change, but they do not suffice to justify it: what the Church confesses is not determined by what she has suffered, nor by what circumstances allow, but by Scripture. And the biblical texts were the same in 1788 as in 1647; what had changed was the mind of those who read them. From the late seventeenth century onward there had been spreading, first among Protestants themselves and afterwards with the Enlightenment, the conviction that religion is a matter for each man's conscience and that the magistrate has nothing to do in it. With that conviction, which was by then that of their century, the revisers read the same texts which the Assembly had read otherwise.
The First Amendment to the Constitution of the United States is commonly cited as the cause, but it is later (1791): the revision and the Amendment are, rather, two fruits of the same tree.
The result, in time, has been twofold: the progressive abandonment, among the majority of the Reformed, of classical Reformed theonomy (the conviction that the law of God ought also to be the rule of public life and of the laws of the nation), and the embrace of the new liberal conceptions of the religious neutrality of the State and the autonomy of the individual conscience. The revision did not produce this by itself, but it enshrined it in the confessional text.

What the text of 1647 rested on. The Assembly cites, for the clause struck out, Deuteronomy 13:6-12, Romans 13:3,4 and 2 John 1:10,11.

What this change shows. It is the first point of entry, and the most significant, because it is made by orthodox men. The idea that enters is that religious error, so long as it does not disturb civil order, is no concern of the magistrate: the State ceases to distinguish between truth and error. The revisers did not experience it as a concession, but as a defence of the church against the civil power. They argued that Deuteronomy 13 belongs to the judicial laws of Israel, which the Confession itself declares to have expired (chapter XIX, paragraph IV), and that coercion produces not faith but hypocrisy. The Assembly understood, on the contrary, that those laws continue to oblige in what they have of "general equity", and that the sword which Romans 13 puts into the hands of the magistrate against "him that doeth evil" reaches also to blasphemy and public heresy. And this was no peculiarity of the Westminster divines: it was the common conviction of the Reformers, who saw in the magistrate the keeper of both tables of the Law and not of the second only. What is new, in 1788, is not the doctrine of 1647, but the idea that replaces it.