I think that the acts that happened were beyond anyone's imagination - who would have thought that all this could be carried with the threat of knives only! - Scary!
About the cockpit door - has it never been suggested to make them sliding? - This way, if locked no-one would even be able to kick them down!
Also in light of what has happened - is there not a facility in the pipe dreams, that allows an over-ride that cannot be altered once decided - i.e. maybe a failsafe button that automatically takes the control away from any of the pilots? ATC could perform autolands / VOR courses etc!
I know this would cause immense problems if it went wrong - but it would stop mad men with no value for human life flying into packed buildings!