i think to avoid the whole risk of making a lot of people angry we should just keep everything nice and abstract.
what if each time you discover a religious tech you got prompted to choose a characteristic of the religion to improve? but if you get a religious tech from someone else, copying their religion, you get what they chose. then maybe set it every city gets the first point bonus, cities with temples get the second, cities with (improovment dependent on chosen characteristic) get the third and cities with cathedrals get the fourth. of course if you decide you want to change your religion it can take a lot of work, cost whatever...
idealy I'd make the religions if the game worked just a little differently I'd also suggest making the religions seperate cultures...