A possible solution: put a better lock on the cockpit door, mason jars for the cockpit crew to piddle in, a small airlock for transferring food/paperwork to/from the cabin, and a sky marshal in the cockpit jump seat. Said sky marshal would be trained at least as well as Delta Force or SEAL Team 6. His job: if someone forces the cockpit door open, SHOOT THE BAD GUY AND CLOSE THE DOOR. Repeat as needed while the pilot gets the plane onto the ground posthaste.
It wouldn't surprise me to learn that there are federally trained employees who can't hit the right house in a firefight. Oh wait - I already know that to be true.
Your allegiance to the government is so strong that you would eliminate the last-ditch line of defense, just because the proposal gives power to a private citizen instead of a government agent. Disgusting.
You really expect that there are enough people out there of Delta Force/SEAL caliber that are going to take a job for any amount of money where they fly around on airplanes all day. TALK ABOUT MIND-NUMBING WORK and low JOB SATISFACTION.
I say, make sure that either the PILOT or the CO-PILOT is armed, they've got to be there anyway. And, once the bad guys know they have guns, there will be NO MORE HIJACKINGS. So, it won't really matter if the pilots can actually shoot accurately (I think they can) anyway.
It's called a deterrent.