And what about Military forces using civilian aircraft:
Falcon-50/900 Airbus 319-310-330 DC10 L1011 DC9 B767?
Not too many military forces operating such equipment strap antishipping missles to 'em. It's as has been said already: so naval ships and (usually, but not only) naval interceptors can easily differentiate between a civil airliner and a military aircraft.
And before you ask, you're right: it won't cover the situation where some sneaky bearded individual with an unpronounceable name cleverly fits a civil radar to his ageing F14.