The Founders, so close in their relationship to Mother England and quite familiar with that history and the Roman Empire, knew full well that religious leaders, most especially in tandem with monarchs, were as capable of corruption and oppressive government as any other.
American exceptionalism, as the Founders intended it, would have the government secure our rights and then leave us alone to govern ourselves and form whatever sort of society we wished to have.
Some Americans opted for theocracy as was evident in some colonies. Others opted for a violent and essentially lawless existence. And it was interesting, that without any interference whatsoever from the federal government, those adopting such extreme societies would moderate them within a relatively short time. All the theocracies were disbanded and had vanished by the time state constitutions were adopted. Those experiencing communities in their raising hell days chose to put themselves under a rule of law.
Short of violating another's unalienable rights, no man can be free without being allowed his convictions and way of life, no matter how narrow minded or unreasonable or foolish or ignorant or hateful or socially or politically incorrect.
Once the federal government presumes authority to reward or punish thought, it is inevitable that it will begin to erode or eliminate certain freedoms.