I'm so going to use that Ender password system for something.
Anyways, for the actual door thing you asked about. You can use an inverter and a redstone torch to make the door always "open", so if they throw down a lever then it won't work no matter which side they put it on. Also I think that you could do a bit of fancy work with RS NOR Latches to create a kind of "check" system that overrides it. You could also use microblocks and redwire to block the current (stick red wire on the bottom of the block and use a glass panel cover to stop the current from going to the door block, and use a corner block/panel strip in front of the door to stop it there), though I'm not sure if that will work seeing as I haven't tested it.