Originally Posted by Malak'ai
Good ol' fashion Witch Trials.
Have one of the higher ups in the church going round random towns and villages putting people on trial for suspicion of using magic. Have them publicly torture a 'confession' from them and those close to them. Then have the poor victoms executed in a horrible way, no matter their age/gender/physical or mental state (before the torture).
That should drive the good aligned characters in the group to start really hating the church. Even the neutral characters should start feeling that this isn't right. The evil aligned characters (if any) will start to either get jealous of, or be spurred on to out do them.
This sort of thing is what you want (although it doesn't have to be exactly witch trials). One big problem with religious organizations is that by they're very nature, they think they're always right (they're speaking for god/gods/etc).
Put the PCs in a situation where the church is doing something that very clearly isn't right, but where the church has a very clear justification for doing so.
God says women can't touch weapons. Church is hanging/whatever a woman for chasing off a bunch of local bullies who had almost beat her child to death. That sort of thing.