Essentially, I believe that I need to work harder to make sure that not only the player characters, but also the players themselves feel convicted to end this church. I want them to be angry. I want them to hate the church and all it stands for.
It could also be possible that the players are either not terribly into the idea of hating the church or could use some distraction from the overarching plot. I would suggest throwing out some unrelated plot hooks -- a small village threatened by giant ants, a newly discovered dungeon to be explored, something totally unrelated to the church -- and see what they do. Make sure they know it is fine for them to switch goals or simply spend a week doing something different. If they jump at the idea, it is a pretty clear signal that nothing you do will make them hate the church. Sometimes players simply don't want to do what the GM has planned for them. Good GMs roll with it.
From September to December of 2012 I ran "In Search of Adventure", a BECMI retroclone set in the Grand Duchy of Karameikos. Wiki -- OOC -- IC