I'm new to the forums, but I've been reading PZ's stuff for awhile now.
It seems to me that one can be scientific and not necessarily be a "scientific racist", but still engage in racist behavior and support policies that are inherently racist. I think that's what PZ is trying to get at. We can all sit back and say that scientifically speaking you can't judge someone's intelligence by the color of the their skin, but some of us will use this fact to support affirmative action and some of us will say that makes affirmative action inherently racist.
Racial profiling is another good example. We may have hard facts that certain races are more likely to commit certain crimes, and some of us think it's racist to use that information to target people and some think it's a moral imperative because it theoretically will lead to more effective policing.