I don't know enough about it, but what are multiple pistol-caliber-sized holes likely to do to the airplane? What about the cockpit wall?
Additionally, what do you do about multiple CCW-folk all pulling their guns at the same time and thinking everyone else is a terrorist? At least with the air marshal program, the guy with the gun will know if there are any other guys with guns on the plane.
And, why guns? Is there any reason that a taser would be a worse option? It seems to me that you'd want to use something that wouldn't damage the airplane, and a taser would also have a far-reduced chance of killing passengers if you were to miss. I don't know much about tasers, however. Would they be an option, or are they just not a possibility?
Why not just put a sleep gas button in the cockpit? If there's a problem, pilots hit the button, put on their masks, everyone else goes to sleep, plane lands, everyone is carried off.