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thomblake comments on A Parable On Obsolete Ideologies - Less Wrong
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If all of science agreed that members of one race really were slighty smarter on average than members of another race, that could be extremely demoralizing for the people of the slightly-dumber race. See stereotype threat. This seems like a high price to pay to eliminate a popular falsehood--I imagine their are other falsehoods that would be easier to eliminate for a smaller price. And unlike religion, there's no long-term benefit associated with its removal.
It's mentioned below to some extent, but if you start with the assumption that there's no systematic variation between groups, then if you see a statistical difference in how groups are treated, that's evidence of a systematic bias. If it turns out that there is systematic variation between groups, the data can be explained without the bias. It's the difference between "Harvard is racist" and "Harvard accepts bright people regardless of race".
Harvard has two responses to these claims: they can continue getting called racist, or they can unfairly admit minorities who don't deserve to get in. Both of these alternatives are preferable to telling a large group with normal human psychology that they are inferior.
Edit: I tend to think it's OK for Harvard to admit too many minorities because I think having the upper class be made up of people from a variety of backgrounds is valuable. But I could see how this could be a problem in other domains, such as cousin_it's mortgage example.
You do realize the top universities (and especially the Ivy Leagues) systematically discriminate against Asian students right?
Its really hard to fight or talk about something like that if one can't just point out that East Asians have higher average IQs than say Europeans.