The point is to retain command of the aircraft so you CAN fly it, instead of a suicidal islamic militant bent on killing the maximum amount of infidels as possible. Lethal cockpit defense is for last ditch defense after a breach of the cockpit door. If you can't maintain command of the aircraft, then you've probably enabled the killing of thousands.
At least you can take comfort in those last few seconds of your life that you didn't have any of those evil guns on board.