Nope. I'm an Ashur supporter so I can't possibly say that the Enclave are evil. They are doing everyone a favor by killing them with the FEV. Who would actually want to live in the wasteland anyway.
One might say everyone in the game is evil, not just the 'powers' of the wasteland, because everyone goes around killing people. The Enclave get targeted as being 'evil' because they are a large force going around killing people, not just one person doing it.
Apart from the scale of killing, the Enclave killing those in their way is no different to the teenage vault 101 kid doing the same.
The difference being that the LW potentially is a "live and let live" type while the Enclave are http://www.youtube.com/watch?v=uaqcGat1WUI.
People tend to not like being deemed unworthy of survival. And if they have the will and the guns... lo and behold, they resist.
Strictly from a Darwinian perspective... the Enclave are ill-suited to the wastes compared to the rest, being "pure" humans. They do not have the adaptations that wasteland humans have acquired to the environment. "Pure" is entirely a subjective standpoint when it comes to genetics and evolution.
So if you get down to it... the Enclave needs to be eradicated on that basis, but Ol' Bearded Chuck will take care of it... eventually. In the mean time... we have their reality-detatched ideology to contend with (read my sig) as well as their propensity to not only use biological weapons, but to use the very bio-weapon that has caused a great many of the mutations they detest.