Jefferson, more than any other founders, was a poster child for Enlightenment thinking. I suspect he would have been happy to see religion and church go the way of the dodo. However, I do think that what set Jefferson and his American colleagues apart from French revolutionaries was their recognition of the danger of the State, particularly one run by the mob. While the French gleefully torn down Chruch and Monarchy and went on a victory lap, the Americans understood that a democracy could suck too. So, while Jefferson probably would have preferred an enlightenment humanist society, he was too smart to think using the state to achieve this goal was a good idea.