I meant Paladins. I think that Maxson said it, but anyways, it was the Paladins who protected the Brotherhood. We do not know much about BoS' history since Fallout, but even if they are not the power they once were, they're still a formidable foe.
I mean, if the Pals are the protectors of the Brotherhood, they need to have experience.
After the Enclave slaughters the first ten villages people WILL resist (see IIWW)
Also, put yourself in the position of an Enclave soldier - a grunt, not an officer. You come in frsh from the Oil Rig, where everything was repaired, in excellent shape and all, where there were people, your friends, etc. Now, fresh from your home, you enter a desolate, burned out city, with skeletons still laying around. Even from behind the visor of the APA this still makes you depressant...
Vertibirds as an air support? I think Vs are far too fragile to perform these tasks, just look at the crashed Verti in Klamath. A possible engine failure (maybe a fuel leak, as the locals said "a ball of fire" (OSLT) will cost the Enclave a precious Vertibird, fuel, ammunition, 2 pilots and a squad of soldiers if there were any onboard.
To cleanse the lands of the mutants using convential warfare, it would take tens of years to complete, and would be extremely costly - count in food, water (extremely scarce in the wastes), ammunition, maintenace of Vs and APAs and guns etc., the occasional hotspot, mutant attack, deathclaws, old corrosive acids etc. It would be far too expensive...
On the other hand...
The virus is an excellent weapon - the FEV only needs to make contact with it's victim to cause mutation. The killer-FEV has the same specs.
The Enclave only needed to obtain a pure sample once, then it could be synthetised on board the oilrig. And, as president Richardson said, they could release it at the Oil Rig, and the air streams would carry it around the globe.
They planned to use it not because they were fanatics. They planned to use it because it's EFFICENT.
BTW, we really dont know much about how strong BoS was at the point of Fallout 2, all we have is a single phrase or two to base on. So this discussion is one big assumption, but fun to read and reply.