If you look at the possible range of aircraft hijacking scenarios, a percentage will lead to unhappy results for some or all souls on board.
The best possible management of a hijacking is to prevent it's happening altogether by making the chances of success so obviously low that even methodical, focussed, disciplined and trained suicidal maniacs will spend their opportunity elsewhere rather than attempt an aircraft takeover.
Prevention is accomplished in part by serious methods and in part by theatrics.
Arming flight crew members falls more into the latter category - adding unpredictable and dangerous components to the arsenal of adversities the hijacker must confront in the course of her mission.
Various creative anti-hijack means might be incorporated (i.e. bolted) into the aircraft itself, whether projectile firing, gas dispensing, skewering, etc. This integrated approach can permit automatic notification of authorities by generation of radio-link alarms on arming or activation, and also permits design of projectiles, line of fire, chemistry, etc. for the geometry and constraints of the airborne environment. Since the weapons would never leave the aircraft without all hell breaking lose from the alarm systems, local laws probably would not be an obstacle. A variety of defensive measures could be available, to increase uncertainty. Personal blasters for cowboy aviators might be similarly secured, yet still handy.
Yes, more junk in the cockpit - dangerous junk. But to a purpose.