Of course the church put a stop to it. It was an army from an SA realm, led by a declared heretic, marching to depose and SA duke in another SA realm. It was really Creed's presence that blew the plan. If Abbigail had called and led the army herself, it wouls have been a different story.
The Farronite thing isn't "stagnation". It's the church defending their territory. And it could have led to a very interesting war, if Farronite hadn't backed down.