Evidence in this case is in an exquisite position for a lawsuit. The administrator's motive is revealed. It could only be an ideological basis for the expulsion from the graduate school. The honesty of the class teacher in giving him good grades can be thanked for this.
The school will try to stonewall it by demanding the right for the administration to make an "academic decision" rather than leave that to the courts. The student should be able to show that there is no reasonable basis for the action of the administrator.
Since it is a private school the real question is whether the court will take the case. Some research would have to be done in order to get the student's complaint before the court. Perhaps further administrative steps within the university's structure would expose how there is a breach of implied or expressed contract here. Students do not go into this program with the knowledge that they are submitting themselves to the ARBITRARY AND CAPRICIOUS decisions of department chairmen to so interfere in the evaluation process of students and their work.
Le Moyne College subscribes fully to all applicable federal and state legislation and regulations (including the Civil Rights Act of 1964; Title IX of the Educational Amendments of 1972 (“Title IX”); Section 504 of the Rehabilitation Act of 1973 (“Section 504”); the Americans With Disabilities Act (“ADA”); the Age Discrimination in Employment Act; the Age Discrimination Act; and the New York State Human Rights Law) regarding discrimination. The College does not discriminate against students, faculty, staff or other beneficiaries on the basis of race, color, gender, creed, age, disability, marital status, sexual orientation, veteran status, or national or ethnic origin in admission to, or access to, or treatment or employment in its programs and activities. Le Moyne College is an Affirmative Action/Equal Opportunity Employer. For further information contact the College’s Age Act, Title IX, and Section 504/ADA Coordinator: Assistant Vice President for Student Development and Multicultural Affairs, 315-445-4525 (voice), 315-445-4767 (facsimile).
http://www.lemoyne.edu/student_life/Student_Handbook.pdf
That typically (my impression only, IANAL) doesn't cover intellectual diversity of the type displayed by the student and apparently held in question by the ed school department chair. But the following excerpt of LeMoyne faculty handbook (pointed to by the Volokh Conspiracy) might:
The following regulations are designed to enable the College to protect academic freedom and the requirements of academic due process. The principles implicit in these regulations are for the benefit of all who are involved with or are affected by the policies and programs of the institution. A college or university is a marketplace of ideas, and it cannot fulfill its purposes of transmitting, evaluating, and extending knowledge if it requires conformity with any orthodoxy of content and method. In the words of the United States Supreme Court, "Teachers and students must always remain free to inquire, to study and to evaluate, to gain new maturity and understanding; otherwise our civilization will stagnate and die."
http://www.lemoyne.edu/faculty_senate/rank_tenure/FacultyHandbook/08_FreedomAndTenure.html
So I would imagine the student might have some basis for action based on breach of contract in the spirit of the above extract from the faculty handbook...