CoZe - your right on point there. What if christanity is founded say... early on, and later on, someone techs Liberalism and builds a secondary christan "shrine" building. Now, the christan nations will have to pledge which shrine they will aknowledge. I really prefer to avoid all flammages.
You could have the missionaries be considered as "New Age Christan" or "New Age Hindusim" which i hope wouldn't cause any real complaints. the only difference, is that the religion that is present will divide between "traditional" and "new age", whatever the difference can be thought of by others who care to think about it. I would be fine with saying something like this:
Traditional gets a SMALLER bonus (or even a negative) with the New Age.
The Traditional and New Age religions interact with one another as they already do. (Traditional buddahists will hate both confuscian New Age and Islam Traditional to the same degree) and the Apostle Palace could be given a vote to classify either the traditional or new age as the "legitimate", which could make the other viewed as an infidel (as a vote, but would initially be viewed as the same religion until the vote occured).
(the same civ should not be able to be both new age and traditional. if you capture the "other" shrine, you should be prompted to choose which one to crush forever)
Just a thought, and if your mad please chill out a few mins before posting as this is just a game and i am only attempting to think of a workable, balanced mechanic (and its other interactions) that have no intention other than another realistic historical element that if properly put in could add an extra element.