Didn't the Enclave try their hand at genocide once or twice? What the Master did is morally grey in comparison. He tried to change people. The Enclave tried to kill them. How can you believe what he did was so wrong it warrants obliteration of an entire race?
The Master thought he could make the world a better place by "elevating everyone to his level". Utter hogwash. Super Mutants were stupid, sterile and eventually not much better than humans, just bigger and stronger. Of course if FEV-2 had not been such a dud I would have a lot more respect to the Master but still every Super Mutant is - once again - sterile and proven to be dangerous with only a handful of exceptions.
Yes the Enclave attempted genocide at least once and more or less allegedly twice, and I see no objection for someone opposing them for that. However, I consider them a better candidate (East Coast branch, mind you) as they have a truckload of other benefits, real plans and technology. The Master didn't have much plan besides converting everyone to big green hulks and roam the Wastes. Sterile and stupid mutants.
Then how about luring them, manipulating them, capturing them and then brainwash them?
There's no reason to exterminate them completely, they can be exploited.
If only it was possible. Only once we have seen a super mutant blindly serving humans, and that mutant was Frank Horrigan who was most likely blindly serving his masters before his mutation.
Super Mutants, especially Nightkin are hostile to humans and dangerous. Nobody willing to spare them is strong enough to approach them.
The Super Mutants have over and over again proven they are a liability. NV is the first time we see peaceful Super Mutant communities, free of conflict, and that's because they don't allow humans to live there. Humans and mutants just don't get along with each other. One has to go.
You do understand saying that means that all species should wipe out all other species in retalliation. I mean just about all species has killed or attacked another. Ghouls, supermutants, cazdore, deathclaws, boatflies.. the least gets quite long.
Cazadors, Deathclaws and the like are not sentient and thus their violence is somewhat justified. But of course, I see no problem with eradicating them, as they are highly dangerous and human engineered mutant freaks just like Super Mutants.