So, the good news is I figured out what went wrong, and it turns out it wasn't Mary's fault after all. I hereby apologize to the spirit of Mary Fields, and hope her ghost doesn't show up to beat the hell out of me, anyway.
The problem was having the girl go in as a holy little nun in training. But if she goes into it as a hellion who is being punished, then when the split happens and she runs off, that takes care of all of the logic things and stops the whole thing from falling apart in the middle.
The bad news is fixing this flaw means I have to rewrite ... oh ... 42 pages.
Bruno is totally going to kill me.