[Catspaw]

He could quite truthfully and charitably say something like "this student understands very well the evolutionary theory of biological origins, and is a good scientist in XXX and YYY and ZZZ areas of biology" [not related to evolutionary theories of origins] and leave it at that.

How would the professor had known this if the student in question never took the class?

[HiTech RedNeck]

The problem seems to be that he is refusing up front to do so and thus discriminatory. This won't be an easy legal battle and could have been set up more powerfully with a student who actually has vested a lot of time in his courses, but it has at least as much logical merit as the prof's position.