Well they kill those they believe are not pure so...
It's always "pure", like their intentional racists or something, in all likeliness the people after the bombs
are quite disimilar from humans, maybe there's a higher rate of infant mortality, or people being born with deformaties, dwarfism seemed common in the earlier Fallouts (back before 3D modelling and animation, lazy people...), slight genetic mutations which have been passed down through the ages. The Enclave want to rebuild, not conquer, they aren't "racists", they are literally some of the last true human beings left alive. Now, I'm not a nazi, but it doesn't meen I can't defend the Enclave right? I hate stock characters and the Enclave aren't just bad for the sake of being bad and racist for the sake of it.
EDIT: The Enclave uniform, or at least the hat, were based on the Imperial Storm Trooper Officers, who were of coruse based on the nazis.