I took the quest from Colonel Moore to go talk to the Great Khans and possibly destroy them if I could. While at Red Rock Canyon, I also took the quest from Regis to try to convince the four advisors to go against Caesar and the Legion. I convinced Jack and Diane, and after I did Karl sent some Legion recruits to attack me. After killing them, I went to talk to Karl again, and managed to get him to admit the Khans are nothing as fighters compared with the Legion troops. This, of course, made the Khans mad so they attacked Karl, but before they could kill him he ran out the back door.

What bothers me is that I got a quest update saying go back to Colonel Moore and tell her that the Great Khans were destroyed. How did the Great Khans get destoyed by removing Karl? The "Oh My Papa" quest is still active. Will I still be able to convince them to support the NCR if I can?

Wow! I have never seen that particular scenario. First I didn't know it was possible to get Karl to confess. Second i have never seen him make it out alive.

Anyway. Talk to both Papa and his lieutenant (I forget his name.) this may open up other options. the only way to get Papa Khan to cooperate is by completing his quest. Alternatively you can get him to just pack up and leave. Both options will satisfy Lt. Moore.

I couldn't talk with Papa Khan , or any one else in the longhouse for that matter. They were all running around with their guns drawn (looking for Karl) and I couldn't initiate a conversation with any of them.

I eventually reloaded an earlier game and this time didn't bother with Karl.

That's what I would have suggested. However if you look in his room you will find incriminating evidence to take to Papa. That will cook Karl's goose.