Hmm Im thinking to make something similar. and i was thinking to make some kind of prefab rooms and on with various exit/entrances of various types and sizes. so the solution i benn thiking of were making an empty object/joint in some point of the doors
that will be common to all doors of same type and the wwill generate the room there. Its some kind of randrom modular rooms.
something like this( At least for what i want i looks like a good idea) You could see this kind of generation in Warframe
http://i1380.photobucket.com/albums/ah198/Krzysztof_Kantoch/doors_zpso73xduna.png
Each door type only can generate a room with same conection ddoor and also a chance to spawn blocked door or dead end of any kind like this i thin you wont have the problem youn have there. But you need to have all the rooms carefuly created to avoid any kind of overlaping