So, here is my issue. I'm doing quest for the republic part 2. I'm asked to deal with Great Khans. I'd like them to join NCR if possible. My reputation with Great Khans is vilified and i killed some chick at Quarry Junction, so failed Oh My Papa quest... Can i still somehow improve my reputation with Great Khans and make em join NCR? I killed Papa, to make Rigis rule but Rigis doest register Papa's death...

Pretty sure you have to get Papa to cancel the treaty with the Legion before you kill him to be able to get them to work with the NCR. Unfortunately for you, that means Melissa over at Quarry Junction needs to be alive - load an earlier save or do without them.