Lockesdonkey,
Actually, I would suspect that, absent a sophisticated immigration model, it's warmongers who will benefit most from freedom of religion since they're the ones who end up with relgiously diverse empires. A small, peaceful builder civ will prbably be full of happy, hardworking, homogenous drones who have no need for freedom of religion, since they all practice the state religion anyway. This may or may not parallel actual history, as expansionist empires are the ones that are often forced to deal with other cultures and religions. I suppose you could also make missionaries serve as a conduit for trade and technology transfer, in which case even peaceful builders might want to welcome them.