Why, you think that Caesar was a better option? Hell you don't even know how the FEV worked; it kills all humanoid (of which I Super Mutant applies) based life and leaves plants and animals perfectly fine, for the record.
Caesar is a better option because, essentially, he's just conquering and enslaving. The destruction of all the culture of the former United States along with its technology is BAD, maybe irrecoverable but humanity would be able to recover from that to a CERTAIN degree. Maybe even get to the point of being able to live in a Victorian era-level of technology even if the resources no longer existed for anything more. We've already seen the effects of things like Caesar on a large scale anyway.
The Mongol Horde, Tamerlane (who was, in effect, a Mongol wannabe), the Visgoths, and the Huns all basically destroyed everything they touched over vast swaths of territory.
Humanity survives.
In the Enclave's case, the destruction of the genetic diversity of the human race on such a vast scale is probably going to annihilate humanity. We've already been reduced to less than 50,000 people before in history and that is a chief responsibility for a lot of the garbage that humans have to deal with today because we've got so much similiarity in our genes (humanity is one of the least genetically diverse races in the world). Now, assuming the Enclave has less than 50,000 people in it (which is a pretty safe assumption) we're talking about making that EVEN WORSE in the future.
What happens if a member of the Enclave has Rose of Sharon Cassidy and her dad's genetic heart condition? A prediliction for Alheizmers? A natural talent for cancer? I'm looking at humanity's future and it's becoming pretty grim.
Let's also point out that the Enclave destroying all of the mutants doesn't necessarilly get rid of the radiation (ala Capital Wasteland). We're, presumably, assuming that the modified virus is done well enough that when humanity leaves the Enclave Oil Rigs that they're going to be immune to the virus due to innoculation. Fine. However, there's no indication that the virus won't mutate in the wild, especially when exposed to Super Mutant D.N.A. In fact, the fact we've not seen any experiments on Super Mutant DNA makes me wonder about how thoroughly the Enclave tested it on mutants.
Testing it on Vault Dwellers and the Tribals is a BAD idea from the start because it's fairly clear that the survivors of Arryo introduced new DNA by intermarrying with tribals from the surrounding area. It's not nearly the sort of closed experiment that they're thinking it is. But yes, even assuming that the virus has no blowback, works, doesn't mutate, and wipes out all other humans BUT the Enclave (who are willing to deal with the low genetic diversity) then we've got other problems.
Labor shortage.
A major thing that is a problem Post-Apocalypse is that, aside from however good the Pre-War government made it, a lot of stuff that's vital to recover infrastructure wise is going to decay well before the Enclave can repopulate itself (and the radiation to die down so they don't become *quote/unquote* corrupted) is going to dissolve. NCR and Mister House has the right idea in that rebuilding NOW is the only way to really begin things anew.
Otherwise, you get the same horrible things happening as Caesar's Legion (all infrastructure collapsing) WITH the problems of the Enclave. Lord Ashur is a **** but he's correct that when you have machinery that's still serviceable, you need to get it running NOW.