Okay the reason is probably this. There are two autorun events in the church:
1- when you finish the stolen statue quest "a matter of faith"
2- when you finish "the sly fox" quest
now what I think is happening is and this is my fault, is that if you finish both quests before entering the church and then go to the church both events want to run at the same time so the game freezes. If you haven't finished the "Sly fox quest" in your game save, I suggest visiting the church first and letting the first event run and Mother Susan reward you for finding the statue and then go on finishing the sly fox quest.