Yes you can. You can either decide to not kill them if you choose to end the game with Yes Man, or you can arranage an alliance between them and the NCR. When you are asked to kill the BoS why doing the NCR quest, you have to talk to the Elder and he will suggest the alliance. Yes. If you side with the NCR and have finished Still in the Dark without overthrowing the current elder then completing Eyesight to the Blind allows you to get the BoS to sign a peace treaty with NCR. Also, doing so will decrease your NCR rep, but not enough to bring it down a rep level.