A point I didn't make in the previous post: For both Calvin and Knox, the sovereignty of the people was limited in one important respect: in their minds, it could be invoked only in defense of proper Christian practice, which, of course, they identified with their own theology. But the idea of liberty slipped its religious harness. By 1625, Hugo Grotius was writing that natural law (a term Calvin used, almost interchangeably, with divine law) derived not from a particular reading of the Gospels, or even from God, but was apparent from man's reason.
Grotius was a Calvinist himself, a humanist, lawyer and scholar, who broke somewhat with Calvinism in formulating his own ideas. Certainly he was a Christian, but he noted that, even if there were no God, the ideas of natural law were true and provable by light of man's reason. The cat was out of the bag at that point. What had begun as a search for a justification for defying earthly princes and prelates became a justification for asserting the right of the individual, to freedom of conscience. As Grotius put it in the twentieth chapter of the second book of his work, On the Law of War and Peace,
It seems unjust to persecute with punishments those who receive the law of Christ as true, but entertain doubts or errors on some external points, taking them in an ambiguous meaning or different from the ancient Christians in their explanation of them. ... But if there should be any weighty error, that discerning judges could easily refute by an appeal to sacred authority, or to the opinions of antiquity; here too it would be necessary to make allowance for ingrafted opinions, that have grown up to form an inseparable part of the human mind, and for the zealous attachment of every one to his own tenents; an evil which Galen says is more difficult to be eradicated than any constitutional disease.
I have a hard time imagining Calvin agreeing with such an argument, which is an appeal for tolerating even "weighty errors." True, we haven't quite reached Jefferson's broadmindedness as far as religious freedom goes, but we're getting there...