Pilots were required to carry guns untill well into the 50s and were actively encouraged to keep carrying them into the 70s during the hijack years. There are no cases of bad things happening as a result of pilots carrying guns.
On the other hand 1 hijacking was foiled when the captain shot the Hijacker dead. It would seam that the impirical evidence of 50 years of guns in aircraft are that they significantly improved safety, not harmed it.
Cheers
Wino