Another factor which I would like to throw into this thread is the number of personnel on the flightdeck.
Years ago many aircraft would usually have four or more crew members on the flightdeck, the extra personnel being flight engineers, navigators, even radio operators in early days of flying. These "extra" crew members must have given an extra layer of protection between the cabin and those up the sharp edge who are controlling the machine.
Perhaps some consideration should be given to having an extra person on the flight deck specifically tasked with security and equipped accordingly.
Reference the previous comments on El Al I believe they first put skyguards on their aircraft many years ago. Not long after there was an attempted hijack and the skyguards immediately shot the hijackers in the air. I don't recall that they have had any problems since then!