I liken Eden to AI like Hal 9000 - choosing extreme solutions instead of inroads. Hal's solution to his problem was to kill the crew because he was conflicted over having to lie to them about the true nature of their mission. Eden's solution to restoring the USA is to wipe the slate clean, and dialogue with him reveals that he feels it is the only way to do so. Eden knows that the original plan to eliminate mutant life utterly failed and yet he's trying to do it again. He isn't adapting to the situation that the world is in, he's trying to pave over it.
As far as Autumn goes, he isn't a saint, but he's the lesser of two evils. Assuming that Autumn was going become a totalitarian [censored] is hard to say - conjecture at most. We'll never know. We do know that Eden wanted to murder hundreds if not thousands of people by poisoning the purifier, something that even Autumn felt was too extreme. We have to remember that the Brotherhood of Steel originally began their exodus in the East Coast by 'cleansing' the Pitt - now known as the Scourge. They weren't just killing Trogs and nearly wiped out the entire city in a single night. This event ultimately changed the Brotherhood.
My point is, don't hang Autumn out to dry like that. He might be an [censored], but the faction he opposes continues to hunt down mutants and ghouls, shun Megaton Wastelanders (opening fire on them), and portraying pure disdain for wastelanders in general - they don't like people outside of the BoS and they aren't afraid to express it.
The wasteland has a severe shortage of saints and an ample supply of sinners.
I take issue with this idea because it is adding to the problem. This is exactly like the Iran/nuclear program debacle, and a lot of people contend that "well, we all have nuclear weapons so why do we care if Iran has nuclear weapons." https://youtu.be/dsGUYnFAvdY?t=4m21s really shed light on this so I recommend watching that - they put it into words better.
It roughly translate into, "well humans are already capable of doing the same thing, so who cares if Androids do it, too?"
That's the problem. Androids aren't human - they're beyond it. Strength, intelligence, reproduction, etc. They're physically and mentally more adept from the get go, and we've seen sentient and self-aware AI choose extreme solutions to problems. Again, we already have a problem with depraved human individuals, why add to the problem by allowing androids the freedom to possibly go down the same road and cause even more trouble.
Humans can tire out and fade into history, an android doesn't suffer from the same issues.