As far as I know, you are out of luck. I had to same thing happen to me. You are forced to side with Mr. Yes Man after dealing with the guy that shot you. I am not done with the game yet, but it seems like it may also ruin my NCR faction somehow.
If you are not too far from your vault 11 save it maybe easier to just eat the few hours. I was 40hrs past vault 11 when I found out about the bug. No way I was eating that much time.
If anyone knows a way to fix Mr. House faction I would love to know about it myself.
No, regrettably I'm in the same boat as you. To go back that far, it would chop off about 30+ hours of profress. Unusual, however, is the fact that my alternate hard save is
right before I enter the robot room in Vault 11! So, it would be easy to back track, if I wanted. Fortunately, I
wanted to side with Yes Man. I just wanted to unload my snow globes on House before I killed him.
Oh, well. Thanks for the input.