On Sept 11 F-15s where enroute to "intercept" a United 757. At this point the twin towers where both in flames and the Pentagon had been hit. Thousands dead and dying. The United 757 was on it's way toward Washington DC.
It did not take rocket science to figure thousands more on the ground where about to die, killed by a 757 guided missile.
When it became obvious the F-15s would not "intercept" in a timely manner, two airborne F-16s where sent to "intercept". Before the F-15s or F-16s "intercepted", the United 757 guided missile crashed short of it's target, saving thousands of lives on the ground.
Once an airliner cockpit is taken over, the jet is now a weapon. That's the reality of 9/11. All the passengers and crew are dead people (once the cockpit is taken over). Do you really think an order will not be given to shoot down an airliner on a bee line for New York, Washington DC or Three Mile Island Nuclear Power Plant?
The choice is shoot down the jet or allow it to complete it's mission, the plane load of people on the 757 guided missile will die in either case. The shoot down will save thousands.
Conclusion, prevent the cockpit from being taken over. How? Arm the pilots with pistols.
Or would you rather just let the jet (guided missile) complete it's mission?
There's more important concerns than your unfounded fear of pilots carrying guns.