The problem with this thinking is that the assumption is that all attackers are going to now seize the plane to crash it into a building. If the attack is a suicide attack then the correct thing to do is allow everyone on board to die if necessary to save more lives.

But if its just a fruit cake you wants to go to Cuba, you are now writing of all the passengers lives when they may otherwise be safe.

perhaps if there were some way that if both the pilot and co pilot aren't flying, the plane can't be controlled from the cockpit. some sort of recogintion system that won't allow unauthorized pilots.