I agree, ITS INSANE. Sorry to crush your hopes. I will never go on one of those days again. I was there the day before and the day of Physics Day and the difference was like night and day. I vow never to go that day again.
First since the crowd is all high school kids, most of them like to ride coasters so the wait's are generally long. Last year was no exception. It may have had something to do with the fact MF rolled back on physics day, but still walk On's for Mantis, Magnum, and Raptor the day before turned into hour and a half waits. The wait to ride just one of these is how long I waited to ride MF the day Before!
My class's physics trip took place another day (the Monday when MF wasn't working). It's just like any other day at the park, except I had to carry around a calculator, pencils, instruments, and worksheets to do physics problems.
To answer more of your questions, as long as your get your work done, you can ride all day unless your teacher makes you attend a special session. Season Passes were accepted in my case so I imagine they will be in yours. I was the only one in the entire school that had a pass (What a bunch of weirdo's who went to my school ;) )
Still a Bad day at CP is better than a good day at school :). I'm not saying it's bad, just abnormally crowded for a weekday in may.