I'm pretty sure Alaster can get back into at least some semblance of good graces with the rest of the Church by denying that he was ever a Prophet and that he only claimed such to rally support against Jonsu. Of course, such a claim would be up to you.
Alaster is a Kabrinski. There are a handful of nobles on Dwilight that would oppose a Kabrinski if they said the sky was blue. Very vocal opposition. So I'm not sure how this will all go down. I can tell you that some people won't be very happy when this is all over.
