"WestCoast, the scenario I have in mind is a commotion in the back and the flight crew opening the door to shoot who"
Let me assure you, that will not happen. We don't open the door in the situation you speak of, this is rule number one. The tenant of anti hijacking security post 9/11 is that the door remains closed if there are any problems. This being true if the crew is armed or not.
The area of responsibility for FFDO's is the flight deck and nothing else. One of the briefing items during the crew brief many add is that the F/A's are on their own should something happen, something they already know. The FFDO's job if there is a disturbance to protect the pilot flying. Keeping the door closed is the primary way of doing so, should the door be breached, then the weapon takes over.