This is a bad idea, even if this professor is being unfair.
You should not seek honors from people whose honor you do not genuinely desire.
No disagreement on that. A reading of the full article reveals the prof requires anyone desiring a letter of recommendation to give his opinion as to how life originated. These are the basic problems with that:
The letter is granted or refused based on the answering of the question, not on the ability of the student. Imagine asking if the student was gay or not before deciding.
The prof wrongly states that there is a connection between the ability to be a good doctor and belief in evo. This is false. If it were true, all doctors who believed in creation, Jew, Christian or otherwise, should not be licensed.
The student, if creationist, is given the option to lie or tell the truth. If the student tells the truth, he is penalized. Therefore this device --by design-- encourages lying.
Dini is setting himself up a self-appointed judge and jury. This is abuse of power. He has the right to grant or deny the letter and with this I do not disagree. When he ignores the brilliance and/or accomplishments of a student because of his personal bias, he is using his position (a position in a state institution) to discriminate against, as he sees it, religion.
Didn't we all shame the USSR when they used atheism and evolution to keep dissenters from good jobs and schools? Now we are doing the same thing!