Simple answers.
- let the pilots who want to, carry guns
- let the flight attendants who want to, carry guns*
- provide gun training for those who need it (remember, most pilots are ex-military
- put better doors on the cabins
- have Sky Marshalls in plain clothes fly in groups of two or three on some flights. Note that to be effective, they would not have to be on EVERY flight. The trick is, no passenger knows which flights they're on.
*preferably in thigh holsters that require hiking the skirt up to get at them...but I digress.