Update:
I found a workaround. Go ahead and try it - it may help you too. Just, maybe create a new save file in case it doesn't.
I wandered and found a few more chests and finished up the couple of open sidequests I had. Thought, well, maybe going back will have changed things.
It didn't.
I went ahead and initiated the peaceful solution dialogue again and ran back through the door I came in. Run back a bit and they lose interest in you. My companions did their dialogue comments and we left the way we came in. I moved forward in the quest, talked to the ambassador, talked to the Mermaid's Den girl, then went back Ygwulf's room.
It was now empty, I could loot all the chests and things, and could exit through the correct door using the key.
Hopefully this doesn't come back and bite me later when they patch it.