They could just target specific components of the system (for example disable comms) and cause an accident without actually trying to fly the aircraft.
Well, sure they could perhaps do something to something.
But how much could they do to safety critical systems ? I suspect the numbers plummet dramatically, if not to zero.
How much could they do to safety critical systems that the flight crew could not overrule by flicking a switch or pulling a CB ? I suspect the number is exactly zero.