Yes, Darwin lived in the 1800s, of course he was racist. However, favored races in his Origin of Species book refers to groups of animals; human evolution isn't in it.
Additionally, it was a banned text in Nazi Germany.
Further, even if someone could justify killing people for the sake of evolution, it wouldn't make the theory wrong; scientific theories like that have no inherent morality, and it is our responsibility to not abuse them.
If the ability to use it to justify killing did make something wrong, nearly every religion, including Christianity, would be immoral.