Some people surely do commit the naturalistic fallacy here: Simply to say it's "unnatural" isn't an argument. Couches are unnatural.
The worry that genetic enginerring might "damage the human race" is quite different, however, and I for one take it seriously. The worry, very simply, is that we don't know what we're doing and that the costs of mistakes could be horrific. I'm not sure what evolutionary theory has to do with it. Perhaps the idea is that evoution could somehow correct the mistakes over time. But (i) that could take a very long time indeed; (ii) human reproductive success isn't driven by the same kinds of things now that it used to be; and (iii) evolution isn't going to resolve the problems from which the actual people born as the products of misbegotten engineering suffer.