I have been looking at the civics code for a little while trying to start a balancer, and It is possible to 'psuedo-obselete' the temple with a civic.
Mainly, with each civic you can apply a happiness/unhappiness bonus if a city has a certain building (Nationahood's +2 happiness with Baracks uses this). We could assign to all of the religious civics a '-2 unhappiness with pagan temple' or some other thing to balance out the happiness given, that way the temple would 'obselete' except for its culture which could be considered to be that religion 'adapting' the pagan religions to itself and itself to the pagan religions, as Christianity is famous for.
Furthermore, we could also give civic 'free religion' only a -1 happiness to represent the rise of Neo-Paganism in contemporary society.
Also, if we make the pagan temple provide a bit more happiness then other templs that could make the religious civics vastly disliked among the AI, and might help curb the spread of some religions by preventing the AIs from switching to a civic that allows a state religion. However we must be careful, because if we make the penalties for adopting a state religion to high than AIs will never convert, and if they are too low then they will still convert too quickly. Or not, I haven't looked at the AI code too much (I keep hearing Bugs Bunny say: "Don't go up there, its dark"). Eventually I'm sure they will adopt a religious civic so they should convert.
EDIT: another thing we can do which should not require too much effort, is make it so the Pagan temple can only be built in civs with Paganism as a civic, to stop the construction of Pagan temples in the modern world, which if I am correct doesn't really happen. This might take some SDK work, as I know you can restrict units to civics currently, but I might have to adapt the SDK tag for this over to buildings too I'm not sure, ultimately I might just need to adapt an XML tag from the CIV4BuildingsSchema.xml file. I'll try to look into this sometime today, but right now I really should be doing Calc Homework...