I assume that what bothers Chode is that you said "only" Christianity will remain. Again, I don't think this is really what you meant. Only it will remain in its current (close to Vanilla) form.
I think that part of what is odd in TAM right now is that the same civilization can have founded all of the religions. It's okay for the same civ to found Olympian gods, Zoroastrianism and Christianity. What's strange is for the same civ to found Heliopian Gods, Olympian Gods, Mesopotanian gods, etc. These religions were so much a part of their life that it wouldn't occur to them to choose between Olympian gods and some other pantheon.
So I think we need some way to make sure that each civ only has one early civ, although of course it can have more later religions.
Similarly, it is weird when Mesopotanian Gods is founded in Egypt and Heliopian Gods in Babylon. Notice that people keep saying that they can't think of Egypt without "their religion" and Greece without "its."
So I think there should be a series of religious options that occur as you go down the religion branch of the tech tree. Somehow when you research polythism you should have the option of being polytheistic. Similarly with God King and some other options. I still think the easiest way to do with is probably with civics, but I would be happy to think of other solutions, perhaps ones that involve graphics changes when you become polytheistic, etc.