Does that really justify murdering all of them? From an objective perspective what has the enclave really done in all of that time other than hide in bunkers and conduct nefarious experiments?
Justified on its own? Not necessarily, but when you look at the Capital Wasteland as a whole, with its rampant mutations, hostile humans (which make up the majority of the pop) and individuals who blow up towns for sheer enjoyment, there isn't alot that shows how progressive they are.
The point though, is that Eden's purpose is not to wipe out the wastelanders, he wants to take care of the hostile mutations and begin the process of rebuilding the landscape unhindered. The wastelanders just get caught up in the mess.
The FEV is also a decisive knock-out to the growing power of the Brotherhood on the East coast. Which the Enclave also must defeat.
Besides that, Supermutants will not just "die off" by themselves. They can only be killed in a reasonable amount of time through military action, and there's probably just as many of them as there are of the Enclave. Once again, the Enclave would have to fight them and lose men in the process. Not only this, but the rebuilding process will be significantly more difficult if every few hours a deathclaw or some random wasteland abomination wanders into the construction and settlement areas as well.
But if you value the wastelanders above all else, then anything I've said is obviously not going to be a good justification and nothing will be. You either agree or you don't.
Even if FEV was used locally the Enclave would still keep finding only tribal villages and such and actual factions like the Pitt are too large to be taken over with what the Enclave has left.
Opening and using Vault 101 would provide a good boost to their population, plus as you know, I believe that Eden's virus wouldn't wipe out every wastelander. Those who were relatively unmutated would survive to be incorporated.
Without having to deal with the raiders, rogue wastelanders and mutants, in my opinion it comes out just as well. The Pitt isn't a threat at this point and it will be awhile before they reach the strength to become one, and that's IF Ashur would be unreasonable enough to not attempt diplomatic negotiations. The Commonwealth is concerned with itself alone and indeed could be a valuable ally or even incorporated into the Enclave's new state based upon their technological advancement. The MWBOS is "in decline" in the Midwest (thus not much of a threat at the moment) and both they and the Legion act as a buffer to the NCR in the far west.
So it will be quite some time before the Enclave has to deal with a rival hostile state. With their rate of production, they would be well on their way by that point. Even if it comes to all-out war, the Enclave has been the only faction to develop biological warfare, they'll likely think of someway to ensure their victory.
The CW is really an excellent position for the Enclave to rebuild itself strategically.
I'm not saying that Autumn is wrong, I just believe that Eden's plan is a more secure plan. I just don't trust the wastelanders or believe that its a good idea to take on the problems of the wasteland by fighting them head-on.