There is no necessary contradiction between anti-slavery and racism; one can be against the ownership of one human being by another while still believing that race is a useful concept and that it is possible to build a hierarchy of races. Darwin does seem to have believed this - there are several passages in The Descent of Man that clearly set out a difference between the several races :
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"There is, however, no doubt that the various races, when carefully compared and measured, differ much from each other, - as in the texture of the hair, the relative proportions of all parts of the body, the capacity f the lungs, the form and capacity of the skull, and even the convolutions of the brain ... Their mental characteristics are likewise very distinct; chiefly it would appear, in their emotional but partly in their intellectual faculties ..."
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A few pages further on, he sees the massive death rates that occurred on contact as being a natural, evolutionary, result of the encounter between superior and inferior groups.
Darwin's ideas certainly influenced the development of scientific racism. However, the doctrine had existed in some form since at least the 18th Century. Ordinary common or garden racism is, of course, far older.