I don't doubt that that's true - there have been and always will be ruthless pragmatists. But, to my mind, they were more the exception than the rule. And I think there's a fair bit of difference between saying "this church sucks, I'm ditching it" and "religion and politics don't mix". As I understand it, medieval morality was basically 100% derived from faith, and so saying the above would be the medieval equivalent to saying "morality and politics don't mix". Do many modern politicians believe it? Probably. Would any of them say so openly? Hell no. Same goes for the medieval version.
I think heresy's a good thing for BM, I think it'd cause more religious conflict - you see that IRL, in that Abrahamic religions tend to hold pretty harsh grudges against each other in spite of being very similar, but at the same time are basically apathetic to outside faiths.
And yeah, I can see that there are like, huge reasons not to allow for state religions or whatever. There is zero gain for a ruler in doing it. Giving a faith a significant foothold is basically just ceding your own power for no gain, especially since the default stance of "all religions are equal, like I give a !@#$" is not only tolerated but lauded. But again, I see that as being part of the problem, not an excuse for it. I think that player culture and game mechanics exist in a viciously reciprocal cycle.
Correct me if I'm wrong, but almost all major medieval conflicts were at least partly religious in nature. This was the era that spawned the Crusades, after all. If ever there was a time when religion and politics mixed, it would be then.
Also, I just think the game would be more interesting if characters actually put some more weight into their faith. I don't really see the point of having religions if 99% of the playerbase is just going to say "they're irrelevant and I'll destroy anyone who tries to make them relevant"
