Before Fallout 3 we would have also thought the BoS would never give a shit about the Wasteland or those living in it - unless you consider Tactics which strayed too much from the lore in parts. The BoS was more about self preservation than anything else. When answering this question I think to myself "What would Bethesda do?"
As stupid as that sounds. Because that is really what it comes down to. Would they think it plausible for an ex Enclave scientist to work for the NCR or other factions? Would the NCR known that the scientist was from the Enclave? Maybe their past is a mystery to the NCR? You name off a bunch of lore reasons that Bethesda would most likely ignore. You are 100% correct in your statement despite that.
It would be no different than Arcade going to work for the Followers. I wouldn't automatically dismiss something that is plausible. When determining what would happen in future games you have to be a little more open minded. Blindly adhering to what happen in the past is a bit boring. I'm not saying disregard lore. I'm saying add to it when appropriate. Based off the information we currently possess we could assume most of the Enclave members were killed, yet the Remnants showed me that there are still plenty of those guys in hiding, most likely integrating with the rest of the Wasteland in the process, whether that be joining up with various factions or not.
So we know there are at least 1 or 2 separate Enclave bases elsewhere besides the ones in the original games. One in Chicago possibly. Hopefully not too many more because they have been overdone to death, but that isn't the question. If we work off the assumption that one scientist wasn't the hugest fan of the Enclave, he was a member nevertheless, they get destroyed, Remnants are scattered across the Wasteland, with many Enclave members gong into hiding; Does this leave room for a few to survive, or do you still agree they would have all been wiped out? At one point the BoS would have been a possible ally during the Battle of Hoover Dam, so Obsidian thought it possible to talk sense into stubborn factions with long held grudges.
All that being said, I'm not only thinking of vertibird tech here which would be duplicated even without the Enclave. There could be other technology that would be important for the NCR to get their hands on. Why kill a scientist when he can be a slave? Put a Slave Collar on that fucker and put him to work. If he screws up you blow his fucking head off.
This is all irrelevant since Bethesda has ruined the franchise but that wasn't the question.