Maybe teach critical analysis in the primary schools. Heck, use the Writ as source material. "How do we know the Book of Pasquale is true? Today in class we will learn how to prove things by experiment".
Gradualism might or might not work. There's already a theological wedge issue about Creation (can't go into details, spoiler) that opens up discussions which, starting with orthodoxy, lead straight into fundamental questions.
Tararoys wrote:This is why Staiyner and the Bretheren have been emphasizing tolerance for centuries. Staiyner is also pounding a personal relationship with God as one of the central tenets of the Church of Charis. Between those two concepts, the conclusion once a few more heresies start showing up is "that dude's personal relationship with God is really weird, but I'll tolerate it" instead of "Kill the heretic!"
If Charis can make the doctrine of tolerance stick in it's own lands, it has a chance of weathering the storm more or less intact, with most of it's populace grumpily arguing points of doctrine instead of hacking each other to bits with swords. If they can move carefully enough, then, by increments, the revelation that the archangels were people will be just one more step in a long journey,. Sure, it'll be a weird belief,, but by then so many other weird beliefs will be crawling around that that one won't trigger a war.
But let's assume the worst: there is a whole round of vicious religious wars lasting hundreds of years, like what happened during the Christian reformation. It is possible that, like the Catholics and Protestants, safehold will settle into a truce of mutual exhaustion, where the majority of people will get so sick of the bloodshed on both sides and tell their respective extremists to go to hell.