I've always thought a Religious Victory should be easier in the early-to-mid game, then become increasingly harder to achieve as Civs start steamrolling towards Science Victories.
All VC must be balanced to be achievable at around the same time, from a gameplay perspective.
Perhaps Science could be a defense against Religion in the same way Culture is a defense against Tourism?
That would make sense only if we see Religion as deterrent to learning/science. I think that is not alywas the case, in Europe/US we sometimes forget that the concept of religion is broader than we think.
Recognizing such a system would probably be a nightmare to balance, it would best mirror humanities growth from worshiping the moon to walking on it.
I would rather see the evolution from paganism to a structured belief system, leaving science to do it's own thing.
Of course, I do agree culture, science and religion need to have some ties to each other. I would expect you will need some amount of each to achieve any victory condition. Some ideas:
-Secularism: Reduces faith generation, increases

science generation. Reduces the spread of every religion to cities of your empire.
-Religious pluralism: Increases

culture generation. Increases the spread of other religions to the cities of your empire.
-State religion: Increases

faith generation, reduces the spread of other religions to your cities. Allows you to build units/districts/buildings with faith.
Last, but not least, different victories in Civ are a way to allow different aproaches to empire-building. They do not mirror, nor try to, real world victory conditions. If sending a spaceship to alpha centauri or having a dominant culture award a victory, I see no reason why spreading you religion by peaceful or violent means, to every empire in the world, should not.