Did the professor threaten him in any way? If so, how?
The professor threatened the student that he would not get a letter of recommendation, which is required for medical school, unless he disavowed his religious beliefs.
I know you'd like to think of this as something other than a threat. But it is a threat.
As an analogy - consider how you would feel if you were counting on my co-signature for a home loan and had already made arrangements in your life for that home and then I said to you, "I will not sign unless you disavow your religious beliefs."
That would be a threat, but because it was not associated with public funds it might not be actionable by the DOJ. But try the same scenario where I am receiving government money for salary and part of my job is to co-sign such loans. Now the government has a special interest in making sure I do not violate your civil rights.
Or the flip side which is closer to the case at hand, what if the home loan was a government loan?
You are in error on two points. One, this professor's recommendation is NOT required for medical school. Two, the request for a favor must include an affirmation of a scientific theory, not a demand disavow a religious belief.
The fact that, often, reality is in conflict with certain religious beliefs is a problem for the student to resolve, not something to punt to the world around him.
That's not a threat and it's a very weak, if nonsensical, analogy. How you've decided this specific student was threatened by this specific professor is way beyond a stretch. It is, in fact, halluncinatory.
Fact is you want this professor removed and prosecuted because he's not a creationist. You don't care about the far-reaching consequences. You've marginalized yourself.
This isn't the article. The student seems not to even have asked for a letter.