Two comments in response to this thread. Firstly those guys up front probably opened their cockpit doors because they thought they were going to land at another airport where negotations would be conducted - not flown into a building.
Secondly if you do completely seperate the cockpit what about other safety issues - in the last 12 months a 757 co-pilot was incapacitated by a lightning strike - what if it had been both flight crew? There are also instances of crews being overcome by fumes. Also how will crews evacuate, view engines etc from the cabin?