As most had fled to East, I suppose the Enclave only left a small detachment to guard Navarro. The Enclave is a force that wouldn't be taken down by some ignorant peons in a fair fight, it's pretty obvious that Navarro was badly undermanned when the NCR swooped in. Arcade says he was born "years after" oil rig incident, and when Navarro was destroyed he was old enough to have some actual memories of the place. Thus I don't think Navarro was in a good shape then, I imagine a lot of troopers just deserted instead of waiting for inevitable doom.
What I more meant, was NCR can't do a thing without it absurdly outnumbering the enemy, hinting of lacks in strategic thought. Plus the NCR is already stretched thin, the deathclaws will die by other means by the time NCR can spare any time to deal with them.
Even if Navarro as undermanned when NCR took it, the base has very powerful defences. Even a handful of people with Advanced PA can put up one hell of a defence. Yet NCR still managed to take it. They could have lost many doing so but that is never stated.
NCR captured Helios, fighting alot of people in PA armed with energy weapons and gauss rifles. Yet they didn't lose thousands of people.
The NCR troops in the Mojave could take them out. It's just they have way higher priorities then killing some deathclaws. Really what would be the point? What is minned out of the Quarry can't even be sent back to the rest of NCR because the rail line was never finished.
NCR's priorities would first be. Contain the Legion on their side of the Colorado. Hold Hoover Dam. Get control over the Strip and the area around that.
Maybe not "thousands" per sey. But certainly hundreds. The Brotherhood at Helios was outnumbed 15 to 1, and they still held on for awhile. Its just that the NCR kept sending wave after wave of soldiers into the meat grinder.
Same thing for Navarro really, and they had the Brotherhood to back them up at that battle. Not withstanding that Navarro's probably had a skeleton garrison at that point.
Where does it say the Brotherhood helped NCR take Navarro?
NCR out numbered BoS greatly but it's never said how many were killed. Rangers with sniper rifles could handled some deathclaws.
Deathclaws are not as smart as humans. NCR could easly deal with them, if they wanted to, and I doubt hundreds or even thousands would die clearing out the Quarry. A couple Vet Rangers would have no problem.