Academic freedom entitled BYU professors to teach whatever they want, which is fine. The problem arises when the professors think they are correct--and the prophets are correct only when they agree with the professors.
The conflict between intellectuals and prophets makes ongoing Church affiliation problematic. The affiliation confers a quasi-authority on the teachings of the BYU faculty, some of whom apparently actually believe they have been hired by the prophets to guide the Church. For some people, the 14th Article of Faith is a reality.
Even if the Church does not divest BYU officially, Church members should recognize that when there is a conflict between the intellectuals and the prophets, we should choose the prophets every time.