Pilots carried guns for longer than they have been banned. They were REQUIRED to untill into the 50s, and were actively encouraged to do so during the hijackings of the 70s.
I know of no cases where anything bad happened as a result of pilots carrying guns. I can point to one hijacking that was stopped when the hijacker was shot dead by the Captain (American Airlines DC-6 in the fifties)...
It certainly couldn't have made things worse on Sept 11.
Cheers
Wino