What I want is that when you enter a house, you will get a small message on the top of your screen telling you that you are trespassing. While trespassing you are able to wait, but may be interrupted if the owner NPC, or another NPC that makes sense finds you (just like a creature would interrupt your resting in Morrowind). Sleeping in an owned bed could work the same way, if you get caught your sleep will be interrupted and the NPC will call the guards.
When attempting to wait or rest in an owned house/bed, there should be a message in the rest/wait menu telling you that you are trespassing, or sleeping in someone elses bed. This should, however, not stop you from doing it.
If the owner NPC is dead, then you can use his house without being stopped by an owner that's no longer around.
What do you think about this?