Well, I wanted to answer yes just because of the creationists line but I do think it has to depend on the story. If we're going future humanity then yes, evolution should be respected but could be taken in new directions. Evolution of course is all about selection pressures so if the story takes humanity to some crazy other-world colony where the selection pressures are vastly different then future evolution has some interesting paths to take. Likewise, if we're talking about aliens that evolved on some other planet with different selection pressures then evolution could have taken a very different route. However, I think a good science fiction writer would probably consider the environment of a world when considering how the creatures native to that planet were presented - whether you consider that they've evolved to be that way or were designed to live on that world by a particular deity/higher power/supreme being doesn't really make much difference.