Lets assume that the Enclave happen by some children. The Enclave do what they do to any Waster, destroy them, with flashy guns. Wasters are Technically Americans too, not just the 'True, proud and honorable Enclave.' The Enclave is just one big bully, really. "Do what I say, or I'll pound you one" is their motto, except, they'll pound you one anyways, because you're a "Threat." If you're not Enclave, you aren't worthy to live. That's how it is, no matter how you try to justify anything, that's how it is.
According to them, Wastelanders are decidedly Unamerican, and therefore should be destroyed.
The argument devolves to one of motivation, and the extent of which a government will go to reach their goals. If the Enclave truly believe in the future they support...Mom and God and Apple Pie..., then they would feel morally obligated to use whatever force necessary to pursue that vision. If some folks have to die in the process, so what.
The Supermutants, raiders, and mutated beasts have clearly overrun the Wastelands. Nothing can change until security is established. The BoS obviously can't handle it. Perhaps the Enclave can. So far, so good. As far as the racial thing...the mutant thing, well, history clearly shows how that can be an epic failure, although such a thing can rally many to the cause. If I were a Wastelander, I think I would be greatly interested in having every mutie killed.
Regardless, The enclave COULD re-establish some sort of unified society by regaining order and repairing the purifier, and they could do it long before the BoS could have done. To that extent, assuming that they believe their propaganda, it would be difficult to see their vision as evil, and if the ends justify the means, so be it.
On the other hand, lets look at Bos for a moment. They can, and will use the purifier to bring the most basic requirement to the Wastes. There would still be a security problem, but that may EVENTUALLY be resolved as settlements become more capable of supporting themselves. Could take years...decades.., and in that time, many more will suffer. The BoS, of course, are a bit more interested in civil rights, which is both their strength and their weakness.
So, which is better: A concentrated and coordinated assault against elements that, due to their nature, create a situation in which society cannot advance, and in return, an authoritarian central government; or a loose affiliation of weak entities (BoS and local governments) which maintain a higher degreee of individual rights at the expense of dragging the war against antisocial elements for years, if not decades?
It's an age old political struggle...one which drives Western politics to this day. Here in the US, we have a great example of it, with our current and previous presidents, with contrasting approaches to solving problems.
EDIT:
There are tow factions in the Enclave. The Eden faction seems the more rational...the more idealistic. The Autumn faction seems the more pragmatic, and potentially more evil. I get the impression that if Eden stays in charge, everything might turn out well in the end. With Autumn, probably not. We see this in revolutions...especially the Russian revolution, where the pragmatists tend to purge the idealists.