Ryan,
Ouch! I agree with your idea (that extra time is just leveling the playing field), but I am not thrilled with your phrasing. To refer to some students as "fully functional" kind of makes the other students -- students with disabilities -- sound defective in some way. The way we talk about people DOES make a difference in the way we think about people. See if you can think of a more positive way to describe such things.
Dr. Jane Jarrow