Yes, this is a thing where the good vs. bad thing is divided in the player's mind.
I personally would accept use of genocide if it was aimed to restore something. (Altho I don't accept genocide of any offensive action if the target was never part of the invader)
Funny, didn't Hitler use the same justifications when he exterminated the Jews? "Germany can not survive with the existence of a Jewish people" was a pretty central theme to that whole bit with final solutions. That, however, is why I said in the first place they were being overplayed as the "bad" guys.
Lets put it this way, the Enclave wanted a "pure" human race and the extermination of all mutants, that includes supermutants obviously but also the new ecosystem and the ghouls, and even partly radiated human beings that survived in the wastelands in order to "restore" America of the past. Besides being presumptuous that anyone in the wastes would want the old America back, in my book, that's all patent [censored], since we know full well the wastes, NCR and Broken Hills, could be restored even with a more "impure" humanity alongside "pure" humans.
I don't personally like the Enclave of Eden or Richardson and I think Eden, in my book, was an attempt at overplaying an original "bad" guy who's time had come and should have accepted change from its original direction. For that reason, I love who Colonel Autumn was, in my mind, he was a much better character than was Elder Lyons, when it comes to "saving the wastes" anyways.