DBB, the reason that an Evangelical college can discriminate based on religion, and an HBCU cannot discriminate based on race, is because of the Free Exercise clause. There isn't any counterpart to the Free Exercise clause when it comes to racial association. The government really, really wants to avoid confronting churches about internal religious matters (like who is morally fit to teach young people).
This is a contentious area of the law and it is still developing. The Supreme Court just heard arguments in this type of case this week:
http://www.nytimes.com/2011/10/06/us...0school&st=cse
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