Woah. Sounds like she's used to a very different rehearsal process than what your school is set up to do!
I've been with an "organic blocking" kind of director, where the actors really decide the blocking with whatever feels best for them with minimal direction from the director. I would definitely look for similarities and see if there's a basic pattern that they're following. My guess is that they are. I think that most actors will want to find their blocking nad stick to it for the most part.
It sounds like the playwright's changes are pretty crazy, too. Messing with all the page numbers is definitely difficult to deal with, but it sounds like you have that at least in check, if not under control...
I definitely second that you need to get some backup on making sure actors are not skipping classes. I really had to put my foot down with a student director that wanted to change the schedule without warning and force the actors to stay late just because. I told him no, but he went right past me and asked the actors. It was clear to see that they were NOT pleased and felt forced to do it. I really ended up putting my foot down and telling him that he needed to respect their time, just as they respected his and arrived earlier than called and spent several minutes in silence because he asked for it. But skipping classes goes way beyond that and needs to be dealt with by someone from the school.
Ah, at least you can look on this as a great learning experience...