First (and only) easy fix: make separate blocking sheets. What worked best for me on an original show I did last year was punching holes on the "wrong" side of the page, so each blocking page faces the script page it refers to - then use numbers to track moves throughout the dialogue. Saves a ton of time, when you have frequent rewrites. An even faster fix (though a tad messy, if you're rushed) is to use sticky notes for everything, and layer them on the pages as you go.
About the professor: if she is overstepping her professional bounds - i.e. expecting you to shelve your academic work - she is asking too much, and that should be addressed first through the SM advisor, then through Production Mgt higher-ups, and finally through the department chair and/or campus conflict resolution mediators. You are at the college to get your degree first, and to stage manage for this person second; it is unreasonable to expect you to put aside your school work (taking calls during class or after a decent hour at night, for ex.) for a faculty-directed show. As faculty, part of her responsibility is helping you become a productive, educated adult with the ability to prioritize - the "in loco parentis" part of teaching, basically.
About the reference issue: are you depending on this person for a recommendation in the future? Does she (or will she) have any influence on your future at your school or in the area you hope to work?
About the reputation issue: college theater departments tend to be gossipy places - sometimes beneficial, sometimes damaging. You said that this director is notoriously difficult; that seems to be a point in your favor, as far as reputation goes - by sticking it out, you will prove your mettle. Should you choose to leave the show, I think (and I hope) that your department is understanding of the difficulties this director presents, and will take that into account in assessing your choice and in future show assignments.
Best of luck.
