I'd just love to see video of a pilot and amateur pistol-shooter (sorry, with a minimal amount of training), strapped firmly by his 5 point harness into his largish, fairly rigid seat 18 inches from the instrument panel, whip his firearm out and successfully shoot-to-kill on the first shot (because that's about all the time he'd have) a surprise intruder attacking him from behind.
It's a wonderful theory. But if it makes you feel safer......
I'm speaking as someone who has spent a long time as a professional military and airline pilot, and almost as many years trained to use a semi-automatic pistol (we used to joke that you were more likely to hit the enemy by throwing it at him). Have to agree with ****su. If you want your gun like Linus wants his security blanket, that's great, but introducing them into the cockpit has created additional risks to supposedly reduce others (and if the bad guy gets hold of it while he's still alive however unlikely one might think that is, it's all over red rover).