If your son continues down the Air Force path, I promise you this wont be the first time they get screwed over by the Air Force. Maybe someone at headquarters missed a decimal point on entering their GPA or something, I don't know. If so, that's tragic, but nothing is going to change no matter what you do. While it might seem like your son is special and they've never seen anyone like him, I guarantee they've got a pile of hundreds just like him who applied. That's the hard truth.
Your son is an adult. It's awesome as a parent you're advocating for him, but it's time for him to put on his big boy pants and figure out his future. If he's as amazing as you say he is, he should have no problem earning a scholarship by the end of his first year. It's obviously frustrating, but this is only the beginning of a very long road. Speaking from personal experience, sometimes it's beneficial for your personal growth to eat some humble pie from time to time.