I've tried several methods and there is no way to go through the option to get her to approve of an Alliance. Regis is bugged as well and will not bring up any options about assassinating Papa Khan either. I've been able to complete this quest through other routes but I really want to get the Khans allied with NCR by using this quest.
Here are some things that I've noticed:
1) When you first get the quest to do something about the Khans I picked the diplomatic way.
2) The quest "For the Republic, Part 2" then updates to: "Visit the Great Khans in Red Rock Canyon and either enlist their air or destroy them".
3) I went to the Khans and spoke with Papa Khan. I exhausted all options and in the end he will NEVER join the NCR.
4) I exhausted all the options with Karl.
5) Two things happen here, if I exit the tent without talking to Regis he will confront me and tell me that he overheard me speaking to Papa Khan. He then gives me the quest "Oh My Papa" and tells me to convince people for support. Now if I had spoken to Regis at the table he would have given me the quest anyways. So it seems you get this quest regardless.
6) I've completed the quest by handing the book to Papa Khan about Karl. Karl dies and I get regis support.
7) I get the support of the other two people.
8) The option to talk to Colonel Moore is STILL THERE and when I speak to her she STILL doesn't have any options about forming an alliance.
Now a couple of things happen at this point. If I go back to Papa Khan and talk to him and I can tell him to break the alliance. If you have a high enough speech he will agree on 2 points, or you can do the Followers portion of the dialogue. IF you pick the option to join the NCR he saids no but gives you an option to "Stick Around" this keeps the "Oh My Papa" quest in your quest log. Which still has the option to speak to Moore.
Now if I return to Moore the only option she has is "The Khans have been dealt with and they won't ever bother us". Nothing about an alliance at all. In fact if you pick this option you complete "Oh My Papa" for absolutely no reason.
I really want the Khans to join the NCR for my saves. Please fix this as their no way to initiate the alliance and get the options for assassination.