The way to make do it work is that a civilian profile would utterly suck as a missle - pbviously 9-11 demonstrated limitations of it.

Air traffic control messages and flight paths could help with that but there are complications - especially when sending out radio communication could light themselves up as a target.

Theoretically fiber optics and dedicated communication towers could separate the functions but there would be considerable logistical implications to that and well - even first world nations with a large military budget don't put that high of a priority on avoiding collateral damage.