Currently the game just make it all easy breezy with inquisition, one click and all the "heresy" is gone and everyone would just happily following the mainstream religion. But if you really think about what inquisition is , you don't just get rid of a religion without people getting killed or banished. Game wise, it's way to OP when you burn multiple missionaries to convert the city, just to have one inquisitor come over and nullify all your work with one charge. So maybe inquisition should reduce the city population by a certain percentage, like for example in a catholic city, assuming there are x people following Buddhism, when inquisition takes place, Buddhism would be removed but the city population would also be reduced by x/2.