Another misconception, IMO. Unless the Air Force has 24 hours notice of a drill or something, nobody is going to take a missile anywhere - accidents excepted.
There have already been at least two examples of fighters scrambled and arriving at a location one to two hours after the fact. It had nothing to do with federalizing private employees though.
I'd say the AF would shoot down a plane if they could... I don't think they could get there soon enough to do it though. I'll just let the 9/11 incident speak for itself on that one.
[In case link does not work, picture is of an ANG F-15 darn near inside the wing of a civilian airliner. The F-15 is clearly armed with at least one Sidewinder missle and one Sparrow missle.]