In the E.O. Wilson article, "Intelligent Evolution," Wilson claims that religion has been responsible for some terrible crimes over the centuries. Religion burned Giordano Bruno at the stake, tortured Galileo, and dehumanizes infidels, among other things. Wilson pauses briefly to acknowledge religion's positive attributes, but he all but implies in his conclusion that its costs outweigh its benefits.
However, I would like to put forth the idea that Darwinism is responsible for some pretty terrible crimes of its own. I think Sofie's post on eugenics did a good job of outlining some of the more frightening effects of Darwinism. In this day and age, humans are taught to value other human lives, and generally speaking, those who do not are considered to be sociopaths. Eugenics does not value all human life, it is without a doubt an appalling and extremely offensive idea. And most relevantly, it is a way of interpreting the concept of 'the survival of the fittest'.
Eugenics could be justified using Darwin's theory of natural selection. If the strongest survive long enough to pass on their genes the most, and if this process is for the betterment of the species, then actively preventing those deemed weak from reproducing could be seen as an attempt to work towards that same goal of betterment. Eugenics, through this thought process, could even be called 'natural', or at the very least, helping along or hastening a natural process.
This is more than just mere speculation about the possible costs of eugenics, and by extension, aspects of Darwinism - eugenics has actually done serious harm. As Sofie pointed out, eugenics was behind the forced sterilization of countless women. It has even been said that the Hitler and the Holocaust were influenced by theories on eugenics. If this is the case, then Darwinism has a very heavy burden of guilt to bear. The term 'Darwinism' indicates ways of thinking that grow out of Darwin's theories and writings, and that is exactly what eugenics is, whether modern Darwinists like E.O. Wilson choose to acknowledge that or not.