I'm having problems when I should have the conversation with Regis. Once the mission is added I go the dam to talk with Colonel Moore about the alliance with Great Khans. In conversation with Colonel I decided not to assassinate Papa Khan. The problem is that when I go back to Red Rock Canyon I am not able to have the conversation with Regis to convince Papa Khan to ally with NCR. I do not know if it's true but I read on some forum that you can't complete this quest if motor runner is dead.

as far as i remember papa khan doesnt side with the NCR he only decides to no longer side with cesaer and leave nv, to get the khans to side with ncr you have to kill papa and its regis alone who doesnt mind the NCR and will fight with them

Kill papa is one of the options of the mission. The other option Regis will speak to you about how to convince Papa Khan to ally with NCR instead of the Legion

http://fallout.wikia.com/wiki/Oh_My_Papa