If terrorists are willing to sacrifice their lives for their cause by crashing an A/C on purpose, a gun will not stop them. They will simply assign one, two, perhaps three of their number to take the first rounds as they break their way into the cockpit, and the terrorist pilot will use their bodies as shields.
In the ensuing melee they are likely to get hold of a/the gun, or incapacitate the cockpit crew in another way, and nothing will have been gained. Don't forget, these are dedicated peolpe we're dealing with.
No, the real security measures will have to be taken on the ground and in the factory. And yes, it will cost the airline industry dearly. But perhaps it is time for a radical shake up, just like the ocean liners experienced after WW2, when the long range aircraft started taking over their business over the Atlantic..