Had the student in question signed up for the class for credit, rather than sitting in on two classes and looking at a website, then had the professor either flunk him because the student believes in creationism, or, if he had gotten an A, refused to write a letter of recommendation based on the student's belief in creationism, the student would've had a leg to stand on.
Letters of recommendation are done on a voluntary basis by a professor. The professor can pick and choose whom he decides to write letters of recommendation. However, the student in question didn't even reach that threshold. He didn't take the class. I can't see where he's been actually harmed.
This is frivilious litigation.
Since the student still can choose, there may not be a sustainable legal issue. If the student couldn't choose, there would definitely be an issue. But again there's Federal funding which brings a whole nother factor to the matter. Note that it's gotten Federal attention. Ashcroft doesn't undertake stuff like this lightly.