A stronger flight deck door would help. When was the present deliberately weakened flight deck door last needed for an emergency rescue? Unfortunately this strengthened door could lead to a situation where the pilots sit safely behind the door as the F/A's and passengers are individually murdered trying to force access. Not much fun.
Removal of all potential weapons at a security check point is a non-starter. All that is needed for a weapon, for instance, is a modified ball-point pen (solid steel tip, high strength plastic shank). The World aviation system can not work with the extensive checks that would be needed. Nice idea but would in effect shut down the airline industry. The six pax who got through the security check would not want to pay for the whole cost of the flight.
Properly trained sky marshals could help. We would need a whole bunch of them (what would there duty time be?) and there is the obvious cost. Who would pay, the airline or the government? If the airlines paid we would get more $7.50 an hour, 25 IQ, renta-cops - comforting thought! Does the sky marshal override the wishes of the Captain as an incident unfolds? What size aircraft must have a sky marshal, only "big" jets or commuters as well?
Arm a crew-member? In this case it may have helped and certainly could not have hurt. If you know everyone on the aircraft is going to die you might as well lose just a few to flying bullets because you are going to lose them all if you do nothing. You have an oxygen mask in case of depressurisation, why not a pistol in case of hijack? Liability? Training? Firearm issued by seniority or by ablity?