Dynamic:insane:Maybe airliners need to have some sort of identify friend or foe system in place (if they don't already), but who knows whether a SAM system built in 1969 will be able to observe it.
They seem to have this already, hence flightradar24 and other similar sites being able to identify aircraft in the air.
If some bright spark decided that a secret military aircraft should transmit a civilian-style signature to 'disguise' it, then all aircraft become targets again. I'm sure that the military dudes would not want a nice big electronic bullseye transmitter on their planes.
The only means is to create an enforceable regulator to enforce no fly zones, and these have to cover all conflicts. So what is a conflict? Who can determine what capability any conflict has at their disposal? A complete re write of civil aviation to add to the need for 100% radar coverage as per MH 370. A full re hash of flight routes internationally.