Picture in your mind the cockpit of a commercial airliner and the total amount of room once you are through the door. Then ask your self where to put the bodies as the each is shot without losing the advantage of the "choke point". How many downed hijackers OR passengers before the flight crew has no room to maneuver at all? I am not against the pilots being armed but dammit it is not an end unto itself.
If anything, wouldn't the pile-up of terrorist bodies in the door make it harder for each additional terrorist to try to force his way in? True, it would be very hard for a pilot to leave the cockpit under such circumstances, but why would the pilot do so anyway?