You bring up valid points. (by the way, I see no conflict between my knowledge of scientific theory, and my deep conviction of the absolute truth of the Scriptures.)
The kicker in all of this, is that he (the professor) simply screens everyone for a Faith that he himself agrees with. He treats those who have a Faith which does NOT agree with the idea of evolution as pariahs. As second-class citizens. And it is based on Faith.
I consider the letter of recommendation as an official duty, as the student will not be accepted into the program without one. This makes the "screening" for the letter an official action by the professor. The professor is discriminating based on the Faith of the student. This is wrong.
If he was making the determination on race, and stated, "Unless you are at least 1/4 Aryan, I will not give you a recommendation" everyone would quite correctly judge this as a wicked and wrong method to determine who is granted "approval" to (in an official capacity, mind you) continue in the program.
The fact that he bases his "filter" on whether someone can state that their faith is of a certain sort (not if they understand the theory fully - but that they accept and believe no alternative) is the point that is most heinous. THAT is the reason that he is so clearly in the wrong.
It isn't a point of how many letters he gives - it is that he NEVER gives them to those who BELIEVE differently - regardless of whether they have learned the subject.
Again, I am deeply ashamed of wronging you, and note that you are quite correct in your amplification of your point (fervor versus rational). I offer no justification of it, and sincerely ask for you to forgive me.