Hypothetical question...
If you could look ahead in the Fallout universe and see the future of civilization, and it ends up the constant radiation eventually causes much worse side effects that ruin humanity, and spreads to those previously "pure", would the enclave still be evil? Or would that advantage of foresight show them to have had the right idea all along, kill many to save even more?
I'm not saying the story is set up like that... again, it's a hypothetical.
Here are my problems with this hypothetical:
Firstly, killing many to save more doesn't apply really as the Enclave is a big minority versus the number of others around the wasteland, remember that to the Enclave only those born into their own are "Pure", thus going the Enclave extermination route would effectively only kill off the majority in order to save the "Pure" minority.
Secondly you are removing all aspects of human adaptability. If anything humans in the Fallout world have the ability to adapt to the effects of radiation via mutations, in fact evolution in itself is a form of mutation. The way radiation affects humans ingame is a way that humans can adapt to it and live with it, very much like the way the humans in "I am Legend" adapted to become a new humanity with those traits that resulted from the worldwide bacteria. In Fallout it's even more ridiculous as radiation can actually cause mutations that are beneficial to people such as rad resistances, telepathy, etc. Naturally I am leaving out other factors such as FEV combining with the entire population, as FEV would have to be deployed to cause effects on the populace I don't consider a factor like this when discussing the natural evolution of the species going strictly from the current natural effects found in the Fallout world.
Basically, I don't believe that the current world would inherently ruin humanity as humans would adapt to it and live on. Would humans be exactly the same as before? Probably not, but that hardly constitutes the ruin of humanity in and of itself anymore than humanity was ruined when it went from Cro-Magnon to Homo Sapiens.
Besides the Enclave is one of the most, if not the most, technologically advanced faction in Fallout. Instead of using all their technology and expertise in finding some magical way of eliminating radiation, safely removing the effects of exposure, etc; they instead experiment on anyone outside their faction (Mostly fatally) and otherwise exterminate those they don't capture. If the long lasting effects would somehow destroy humanity as a whole (Turn all of us into mindless ravenous zombies or outright simply kill off the species) the Enclave could have invested a much more different approach as to how to "cleanse" humanity.
No matter how you try to see the Enclave's pov, there is no rationalization to their goals. They can't be right because they simply want to kill off anything that isn't exactly genetically like them. That is racial genocide; immoral, unjustifiable, petty, cowardly and ignorant.
So yes they will always be evil because the reasoning behind their actions are as evil as the atrocities they commit.
My two caps...