It doesn't make sense to me that they could've had this huge, years-long war, almost wiping out the Brotherhood, but then make the treaty you can make in NV between them.
It makes perfect sense given the circumstances:
1) The upcoming battle is critical to the NCR's long term future, a Legion victory will open the way into the NCR proper.
2) Kimball has staked his political future on successfully annexing the Mojave....if the NCR does not win he is finished no matter what happens in the future.
3) The NCR is badly over-extended, and desperately needs all the help it can get.
4) The BoS does not have the strength to defeat the NCR.
4) The other factions, the Legion and House, are abhorrent to the BoS and are not suitable allies against the NCR even if they were willing.
6) There is no scenario for a Independant NV that the BoS is aware of.
Based on this, the BoS has leverage with the NCR, the only faction remotely acceptable to the BoS. The NCR cannot afford to lose, and while the BoS cannot beat the NCR, they
can help the NCR beat the Legion. By sweetening the deal by also agreeing to renounce thier claim on Helios....effectively accepting NCR sovereignty over the Mojave....I don't see how Kimball and Oliver could say no to the offer. All they are being asked to do is suffer the BoS to exist in what the Brotherhood themselves now concede to be NCR territory. In exchange, the NCR gets highly effective reinforcements that they desperately need for a battle that they cannot afford to lose. By making this deal, McNamera makes the best of a bad situation and buys time to either find a place for his chapter in the NCR, or to peacefully relocate to a point outside NCR territory.