MY childs has a doctor waiver from PE and the school says they might not except it, is this legal?

he has asthma and cannot perticipate in the activities or change clothes due to the mildew in the gym's i have been fighting with the school for over a year and the say he cannot get a diploma without 2 years of PE and that the school district has to recognize the waiver from his doctor, they have added that the school district has the final call not the doctor, is this legal????