Perhaps an alternate story would be to have the NCR be able to ally with the BoS before they ask you to kill House, that way they are an asset to Hoover Dam and Mr. House doesn't exterminate them.
Anything really. I just don't think a BoS remnants faction would be really worth it. The Remnants of the Enclave can pretty much go any which way, and its canon that they kick ass and leave. Making them at least something of a force to be reckoned with.
With the BoS, I can't imagine why the remants of the Mojave chapter, assuming there really would be any worth mentioning, would stick around to negotiate with the faction that just blew them up or with either the Legion or the NCR (who both want them dead), nor would I see a reason for House to keep them alive for negotiation.