This is a bit of a tangent, but it seems to me that the only real problem w.r.t. conflicting faith and reason occurs when a particular faith lays down religious laws which are not predicated on both parties following that faith. Islam clearly does this. I don't think Judaism does - what I remember of the legalistic sections of the Old Testament seems to apply only to Jews, and in the modern sense presumably only to practicing Jews. Most of the other major faiths I'm reasonably familiar with don't, although I don't know enough about many (e.g. Hinduism) to make the call.

Christianity seems to be kind of a special case. As I understand it, most of its legalistic provisions are inherited from Judaism in a roundabout kind of way, and thus should really only apply to Christians, but there seems to be a Western tradition of assuming anyone in a Christian-dominated country is subject to Christian religious law.

For a long time that didn't really matter, since the only significant non-Christians in Europe were Jewish and thus responsible for a superset of Christians' secular obligations. As you imply, it only really started to change during the Enlightenment, when freethinkers, Deists, and occultists of various stripes started popping up.

What I'm worried about isn't faith superseding reason in private life, as even politicians have a right to believe in Great Cthulhu if that's what suits their fancy. It's a belief in the tradition I've mentioned, that specifically Christian prohibitions (and various Christian philosophical positions) apply to non-Christians -- and chatter about faith in public life, the United States as a Christian country, et cetera often seems to be nothing more than shorthand for the same.