To be honest, the church is helping and giving food/shelter to a large number of refugees on top of being pals with the island's authority. In a proper game flag trigger where world state will change if head priest is killed, the refugees gonna riot hard againt Noer and it's gonna be a bloodshed.
I did see them on the front line of Sybaris fighting abominations and offering help to Sybaris's refugees so they're kinda all right in my book on that front. They got guts, these religious fanatics.
A necessary evil for now.
Beside, gameplay wise, that's a good way to ruin your Hell/Doom mode playthrough permanently.