Hmm...
Interesting post 747Focal, I had no idea these new doors were the cause of so many headaches.
On the subject of making the doors more secure, why don't they just use two doors in an "airlock" type setup, i.e. : Only one door is ever open at any given time.
That way, when a pilot wishes to leave the cockpit, he can step into the "airlock" and lock the cockpit-side door behind him, then open the cabin-side door. This way the cabin would never be directly exposed to the cockpit. The "airlock" would only have to be big enough for one person at a time, so I can't see space being that much of an issue.