You've laid low a lot of people's hard work into their characters; I doubt they'll be happy about that, especially since they have no in-game recourse whatsoever. There is no "protest" option against the head of a religion and since there are no schism mechanics we won't see someone leading the vast majority of the church away. That is bound to be extremely frustrating and honestly I wouldn't be surprised if people whose characters are more invested into the church (and thus who are themselves more invested by the work they've put in on behalf of those characters) did quit. Hoping against it is a pointless gesture, and that goes for both of you. If you've ever played Diplomacy you know there are going to be actual hard feelings for what you did in the game; the only question is whether people get over them.
Will this kill SA? I don't know, but it is extremely obnoxious. Is this a circumvention of game mechanics? I mean, only in that there is no recourse whatsoever. If you look at this in a historical light, there would be an Anti-Prophet in Morek in roughly *now*. That is impossible in Battlemaster; since roughly half of Dwilight is part of SA, I hope this can in some way move up the timetable on adding schisms to the game.
With that said, are you amenable to an OOC schism agreement? I mean it'd render priests basically powerless at working against the other part of the schismatic faction but it would allow people to roleplay acceptance or rejection of the new "Prophet" while retaining their religion.
Also everything De-Legro said.
There are plenty of options from here. Jonsu may command the Church, but the religion isn't tangible. Its more than the numbers the game tells you in regards to temples and followers. I have always been, and will continue to remain, open to interesting ideas so long as it makes sense for Jonsu as a character. Yes, the lack of a proper schism mechanic sucks, but it has worked against me in the past as well.
And yes Chenier, intrigue. Intrigue lead to this, and good intrigue could fix it again. Easily? No. But taking over the biggest religion in the game wasn't easy either. This thing, played right by the right people could blow up in Jonsu's face, hard.
