Another scenario to ponder (I don't think it has been raised before)...
Imagine a skipper who was qualified to carry a gun, and an FO that wasn't. If the skipper wants to go for a 'physiological' break he surely can't leave the gun in the cockpit with the FO as the FO isn't qualified to carry one. What does he do with the gun? If he leaves the flight deck with it he must be susceptible to being attacked, thus giving a weapon to terrorists.
Will there be a locker in the flight deck? If so, will the qualified crew member have their own padlock to ensure it is only they who can access it?
Likewise, on leaving the aircraft for a nightstop what is done with the gun then. It wouldn't be possible to leave the gun on the aircraft as chances are the same aircraft would not be waiting for them after 1/2/3... days. Does this mean aircrew hotels must now have 'gun lockers' on their list of facilities.
It also seems worrying that El Al apparently considered this option, yet decided against it...