A very high tech solution is interesting, but it would probably be simpler and more cost effective to install a toilet and mini galley in each cockpit and surround the whole lot with an armoured door/bulkhead.
I do not think that it is realistic to tackle the root cause of this particular problem. There will always be some disaffected nutter whether he is protesting about the Middle East, abortion rights or the lack of free school milk.
Depressed of Glasgow