I told her to wait in a room, while I sneaked up behind someone to kill them. And after I killed them, it started a cutscene where I was transported out of the room, and the room is now inaccessible. SO she is stuck in there.. waiting... forever. Will she eventually disappear? Or am I stuck without being able to get another companion forever?

You might be screwed if you told them to "wait."

Try fast traveling somewhere, and then go back to the original place you found them.

If that doesn't work, do you have any saves you can load before the cutscene?

No, it was a while ago. I figured the room would still be accessible so I just figured I'd go back later... And then later I discovered I was wrong.

Did you have them holding any good stuff, or are you just angry about the loss of the companion?

I dont care much for the companion. Just that I cant get a new one because she is still technically following me.

Hmm... I've had a few missions where they take away my follower and insert themselves (a companion quest with Vilkas or something did this). Maybe try getting a quest where you are forced to use someone else as your companion? When I returned, I had no companion following me, and Lydia was back where we first met.

ouch... hopefully they'll fix this because this is technically a bug