Ha! Try telling them that you intend to take him out of school permanently. They have no right to tell you that you "shouldn't" do what you feel is best for your son. We took Ewan out of school about six weeks ago (for other issues entirely) and have been homeschooling ever since. He is now doing the work that his class will be starting in Jan/Feb. When we took him out, we asked the principal if it might be possible to skip him a grade next year if we decide to put him back in school (part of the problem was his steroid induced frustration over his classmates not being as smart as he thought they should be). We got a flat out "no", so we may just keep him out and keep homeschooling. Maybe give him his GED when he turns 16 and send him straight to college classes.
Public schools drive me nuts anyway, but the way they turn a blind eye to boys with DMD sometimes just makes me want to puke. Amanda, I know not everyone is set up to be able to homeschool the way my wife and I are. If you feel you can, I would totally support you, but I know it's not realistic for most parents. My point in this little side rant is to just encourage you to fight to get what you think is best for your son. Don't ever feel intimidated by beurocrats into doing what THEY want just because it makes it more convenient for them.
As for the question of 90 minutes being too much, I will agree with another poster here in that it depends on what kind of PT. Also, I would say it depends on your son. Only you know what he needs and what he gets out of PT. I will say that we don't do PT outside of the home at this point. Ewan is 8 and his heel cords stretch to 90 degrees. We either do manual stretches (30 seconds on each side five time each) or boots for one hour. We try to do one or the other every night, but realistically it ends up being about five times a week. So far, he has maintained his 90 degree angle. We don't plan on changing anything so long as he maintains this level of flexibility. Would that be the right decision for every boy? Probably not, but it has worked for us so far.
There's no exact science. I never allow therapy in school and outside school on same day so that I don't overdue it for the boys. [But we have 5 days a week from Board of Ed.] In fact you should figth for more and shorter seessions each time exactly becuase you agree with them. Take their point and use it against them.