Just started "For the Republic: Part 2" and am stuck on the Great Khan part of the quest. I have already completed "Oh My Papa" (outing the Legion ambassador and having the Khans kill him) and "Why Can't We Be Friends?" and now whenever I go to talk to them about joining the NCR - no new dialogue options are there for Regis or Papa Kahn. Am I screwed, and now going to have to kill all the Khans? That seems to be my only option...anybody have any info?

You don't have to kill the Khans, just getting them to break the alliance is sufficient.
Assuming you want a good outcome for the Khans you don't want them allied with anyone.

They have the best ending for them the way you did it. You'll hear dialogue about how they were all wiped out but you know it isn't true and the end scenes of the game tell their path correctly. There won't be an alliance unless you kill Papa...and I couldn't do it. That doesn't give them a good ending anyway.

I just go in and wipe them out. Quick and clean.

I killed all the Khans...mostly because they were sided with Caesar and I wanted their gear (hunting shotguns, hunting revolvers, trail carbines).