I've thought about this quite a bit, and am really not sure what to say. I can't really follow a lot of your arguments, and disagree with many of them.
However, it seems to me like the biggest disconnect here is that you are trying to use the religion itself as some kind of offensive weapon. Or perhaps to expand your religion by force, but without the support of any government or military forces. That's really not how it was intended to be used. You are correct in that if a religion has a lord and a big temple in a region, and your religion has none, that you will have a hard time getting a foothold there. This is by design. The established religion has all the cards. Do you expect to just be able to walk in and preach for a few days and kick them out? You will need to do a lot more than that.
Game mechanics do not support state religions. You could say they support the established religion, or perhaps the religion of the lord. I don't see how that is unreasonable. If some random priest could walk in, preach for a week, build a temple, and kick out the lord, that would be completely unacceptable. Religion needs options, but not unbalancing ones.
Intolerance doesn't just mean game mechanics intolerance. (Although you do have some of those methods available.) Religion, more than any other game system, needs popular support from the nobility. You need to grow and expand by capturing the loyalty of nobles. Win over the lord. If he won't join you, then go to his neighbors and win them. If they don't want you either, then maybe you need some troops yo help you expand by force. And if no one wants to help you at all, then I guess you're just stuck. You can't be a one-man army of religious aggression.
