So last night, before going to bed, I had a great idea for how to limit early-game religion rushing, and I think I've remembered it. I call it Revival.
Basically, the idea is this - when a religion is founded, you only have X amount of turns to build missionaries. Not sure how to calculate the X - my preference is to base it around the number of cities in the world, but it would probably have to be balanced a lot.
You would also have to turn up the chance of religion spreading randomly, no misisonaries.
Anyway, after X turns, the initial explosion that every religion has, you can't build missionaries anymore. The only way to expand your religion is to found new cities (and even that is semi-random).
So religions stagnate, and the early advantage given to Hinduism and Buddhism is gone.
BUT...later in the game, when new religions appear, and missionaries spread them to new cities, this might cause a religious "revival" of the old religion. This'll cause another X turn of that religion's missionaries to be built.
This SHOULD get the player to want to spread religion as quickly as possible, up to declaring war on other civilizations because you only have so much tiime. Maybe even a Golden Age?
A few historical examples - Early Islam was far more vibrant that other local religions and spread like wildfire, replacing Christianity all over what's now called the Arab world. In Civ4...well, I've never seen Islam become a major religion.
A better example would be Europe during the Reformation. Catholicism was fairly stagnant When the Protestants started spreading in Germany, it triggered a Catholic revival - the counter-reformation, which was also based around a return to an almost mystical, populist form of Catholicism (much better for missionary work). The Catholicism wasn't just vibrant in Europe, but spread across the entire world, thanks largely to the great revivalists of Catholicism in the Reformation, the Jesuits.
I think this would add a lot to the game, but I'm not sure if it's feasible, as I'm not a modder. But it'll give reason to switch religions without resorting stereotyping of religions.