The reason for requiring the second person in the cockpit is so that they can visually identify the returning pilot when he requests access and visually verify that he isn't in distress. Some aircraft have a video system which allows this verification to be accomplished without having to stand at the door and use the peep hole.

The keypad is there so that access can be gained if those in the cockpit are incapacitated or if the cockpit is unoccupied.

The override function is there to allow the cockpit to be defended in a hijacking attempt.

Changing the door design or procedures will not prevent a pilot from crashing the airplane if that is what he wants to do. It wouldn't even be necessary to wait for the other pilot to leave the cockpit or to first incapacitate his. All it requires is a different approach to initiating the crash that doesn't involved a long, controlled descent.