You know what? I have the perfect solution to your little dilemma. There just so happens to be an upcoming expansion for Crusader Kings 2 called Holy Fury. As you no doubt suspect, it focuses a great deal on religious mechanics and holy wars in particular. The thing that would interest you the most, I suspect, is that now characters can be canonised by the church, should circumstances permit it. So in essence you can create a world where Joan of Arc is never canonised (or even born, for that matter), and therefore you don't need to worry your sweet little head about this stuff in the first place.
Unfortunately, we don't have a release date yet, but it'll probably be out around the end of the year. Paradox are a pretty reliable company, after all. So yeah, that'll hopefully calm you down a bit.