Alright, so I'm gonna clarify all this information this in one simple post.
They have no breeding stock whatsoever remaining. Their idea of "pure humanity" and repopulating America with them is ridiculous. They couldn't repopulate with just pure humans. There's literally no Vault population left. Nearly all the 122 Vaults holding up to 1000 citizens (one was overcrowded with 2000) had failed or were abandoned, and only 13 control Vaults exist, and 4 of them are abandoned, so 9. 101 has just over 100, and even that is starting to inbreed and have genetic effects, which could even relate. Secondly, the Enclave only have personnel within the thousands. They will soon run out of stock in a few decades, dooming them and making their ideology and cause pointless, due to the diminishing and dwindling amount of unmutated humans.
This would be the exact same if the Enclave succeeded in 2241 and destroyed the world, leaving only unmutated humans. There would be nowhere near enough people, and nowhere near enough genetic diversity, or even enough people to breed to be perfectly honest.
The Enclave Remnants couldn't honestly regroup and resurrect either, due to their inability to breed significantly. Additionally, the fact Autumn disagreed with Eden (to an extent) and didn't believe in pure humanity doesn't matter. We don't know whether all the Enclave personnel in DC agreed with pure humanity or not. Additionally, if there are other bases throughout America, who have been stationed there since Navarro, they'll most likely hold the same opinions that they did in California.
Ghouls, mutants, and the Brotherhood
Now time and time again, I've seen the statement that "the BOS hates ghouls, etc. too!" No, in FO3, this fact is inconsistent and is only said in one instance, and we all know how Bethesda's writing is. In addition, this statement doesn't make the Enclave morally right and correct. All you're trying to do is balance the two of them, which makes you wrong.
On a side note, since both games (FO2 and FO3) force you to go against the Enclave no matter what (Infecting the purifier or blowing up the Citadel doesn't make you an Enclave supporter, they're just absolutely completely random, pointless options), doesn't that tell you something?
If they're going to follow Autumn and not believe in the pure humanity thing, they may as well just stop their whole "Enclave act", and just integrate and blend with normal wasteland society. They should even drop the whole superiority and government thing, and just instead remove their entire persona. They should transform into a paramilitary peacekeeping force, recruit outsiders, and just use their resources in rebuilding and helping the world.
I'll add more to this possibly.