As I see it, the gun is the last resort method of denying access to the flight deck. On it's own it is useless, but in conjunction with an armoured door, it can stop a suicidal hijacker gaining access to the controls.
Ideally, any hijacker will be overpowered by the passengers and cabin crew- but if not, that should still allow time for one pilot to leave his seat, deploy whatever extra barriers are available (jump seat, whatever) and be facing the doorway ready to resist. If the door is forced (I doubt if the armouring can be made perfect) he is then in a good position to shoot the hijacker.
In any of the scenarios above (passengers/cabin crew held hostage, "traditional" hijacker, etc) the armed pilot does not leave the flight deck, he does not even open the door.
With any hijacking, the hijackers must now be kept away from the flightdeck, at any cost. It is unlikely that suicidal hijackers will identify themselves as such- how do we tell what kind of hijacker we have? Take them where they want to go, but don't give them an opportunity to take control. In the final analysis, if they're willing to destroy the aircraft to gain access to the controls, then givng them that access seems like a very bad idea. Once the aircraft is safely on the ground, throw the firearm out the window if you want to keep it away from the hijacker!