This was a feud waiting to happen.
Especially once all you durned republicans started trying to order around the theocracies. Many of the newer elders, especially the ones from the southern regions, have depressingly little knowledge of how the church really works. Rather than learn about it, and how to do things, they have assumed that the church runs like a realm. i.e.: Those at the top give orders and everyone else blindly follows, or makes a few feeble and ineffectual protests and everything just works anyway.
But that's not how it works in the church. Too many elders are from non-theocracies, yet feel perfectly free and justified to make lots of demands on the theocracies. But they failed to get buy-in from the people who would actually follow the orders. As my character said IG, the theocracies will resent being ordered around by people who are not members of theocracies. People don't like it when they are handed orders, restrictions, and dictates from people who are completely unaffected by these.
Hireshmont tried to get the Crusade by just rallying the elders, without convincing the majority of the actual members that a crusade was worthwhile. So while enough elders went along with it (and I think Medugnatos did it just to get something started in the church), a large number of the full members despised the entire idea. And in this case, the first real trial of it, the Archon system totally failed. This is mainly Leopold's doing by not taking part in the crusade discussion in any way and then publicly refusing to participate after it was called, but he's not the only one to blame. I don't remember seeing too much participation from the other Archons either.
Now we have a thoroughly alienated Farronite Republic and a disgruntled and alienated Niselur. (Although it appears that this separation on the part of Niselur was Leopold's purpose from the start, possibly going all the way back to his rebellion against Turin.) In addition, many of the members of the theocracies are angry at the declaration of the crusade, even though they participated in it.
It is a bit disappointing that so many of the church members, especially the newer converts, have just ignored the church and sided with their secular authorities. It removes one of the aspects of SA that made it so unique and interesting: The conflicting loyalties to both realm and church. This requires a willingness of the players to allow their characters to be subservient in part to the church, just as they are subservient to their realms. If people just blindly side with their secular authorities without acknowledging the conflict between the two sides, then SA becomes just another boring BattleMaster religion that can be safely ignored. It will lead to the church sputtering and fizzling out.
It would be interesting if this lead to a series of splinter variant faiths based on the Stars. I have a feeling, though, that what we will see once the theocracy system collapses, and takes the church down with it, is a bunch of completely unrelated religions popping up. These will end up being the bog-standard boring and ineffectual religions that we see everywhere else.