The professor is not discriminating based on "religious beliefs" -- he is discriminating based on rejection of a basic foundation stone of the biological sciences.
This case reminds me of the Muslim woman in Floriduh who is suing for the "right" to have a driver's license issued with a photo taken in a burqa. The state's refusal to do so is not discrimination based on religion -- it is simply a rational insistence that a photo ID should include a photograph that acutally identifies its subject.
He is discriminating on belief not knowledge.
If you set up an appointment to discuss the writing of a letter of recommendation, I will ask you: "How do you think the human species originated?" If you cannot truthfully and forthrightly affirm a scientific answer to this question, then you should not seek my recommendation for admittance to further education in the biomedical sciences.
He doesn't use the words "correctly" and "adequately". He uses "truthfully" and "forthrightly".