How can one ban religions besides not allowing temples to be built or priests to preach? That is precisely what the Theocracies do unaffiliated religions. There is no much more to do.
You can try to ban anyone from your realm that is discovered to even belong to a religion.
Napoleonic times came influenced by a lot of ideals of the enlightenment age, republicanism tied with Emperor-semi-worship (or personality cult), French revolution, universal rights, anti-clericalism and whatnot. It's everything besides Medieval.
While the French certainly revered Napoleon its not like they abandoned religion entirely.
