No student has a right, under law, to a personal, positive, recommendation from a professor.
I understand what you are saying, however a recommendation is required for medical school.
In other words, if the voluntary nature of a letter of recommendation can be used as justification and excuse to override a student's civil rights - it would be possible to keep any minority out of medical school.
Between the civil rights movement and the establishment cause of the Constitution, the court may issue a ruling that many professors will not like.
He can get a letter from his aunt.
In no way is this student, or any student, denied an education.
The only effect would be that letters of recommendation would become worthless.