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

Some of the reasons why the bolded phrase was removed in the American revision are the following:
1) The new view of religious liberty embodied in the First Amendment to the Constitution of the United States, and the resulting changes in Church-State relations.
2) That many Christians had fled from Europe to the United States precisely because of religious persecution, in search of liberty.
3) That American society, like all of present-day Western society, is an heir of Enlightenment thought and liberalism.
4) That, as a consequence, most Reformed people today have abandoned classical Reformed theonomy.