If you pay attention to his dialogue, you'll see Eden doesn't want to kill all impure people, he wants to kill all harmful mutations (SMs, rad-creatures, etc). But the only methods he sees as actually being effective is the mFEV, which doesn't discriminate between mutations. He clearly states that the death of people with minor mutations are an unfortunate, but unavoidable collateral effect. And I agree with him on that, I can't really see how his goal (ie restore pre-war America) could possibly come about with giant scorpions and SMs roaming about
The FEV final solution isn't the only issue with the Enclave, though. We could take away that plan, and they would still come away just as tarred as they were meant to be.
The Enclave has death squad patrols in the wasteland. They round up undesirables, and execute them.
They lure people into lorries (trucks to you yanks) with the promise of clean, potable water, and then burn them to a crisp with a flamethrower.
Their chief executive officer, a man that receives his share of hero worship on these boards, murders an innocent woman to get her colleague to cooperate. If the main character tells him what he wants to know during an interrogation, he murders him or her in cold blood.
If Vault 101 is uninhabitable, Amata can get caught by the Enclave, where she too will be murdered after ended interrogation.
There are Enclave encampments with Deathclaw cages, but rather than Deathclaws there are dead Wastelanders in them.
There is an Enclave checkpoint, where there is a computer, where you can see the names of members of the "vagrant population," (Raiders and ordinary wastelanders) who have been detained there and executed.
There is a temporary Enclave base set up in one of the sattelite towers, where the ovens are in full service. On the floor below the ovens lie the remains of several wastelanders, ready to be processed.
I could go on, but I think I've made my point. The Enclave is a brutal, totalitarian state that crushes all dissent and opposition, and kills all undesirables. Even without the FEV plan, they are still conducting what amounts to ethnic cleansing, only it is not nationality or race that determines who will be purged, but rather DNA as it relates to the prewar stock.
And even if they didn't do that, The Enclave represents a government that has been defunct for 200 years. They have no legal claim to govern America. The United States of America does not exist any longer in the Fallout world, and people have set up their own small political entities. The people of the American mainland no longer have any obligation to a government that disappeared eight generations before they were even born.
People all know this. These are facts that are readily available simply by playing the game. And yet there are still people, who claim that I have misunderstood the game, when I correctly identify the Enclave as the antagonist in the Fallout universe, and not a force for good. That goes so far into denial of plain fact that it is borderline insane. I can take solace in the fact that the developers (both Black Isle and Bethesda) and 95% of the players agree with me, but I am still extremely puzzled over those last 5%, who seem unable to process the relatively simple story told in Fallout 2 and 3.