is encouraged vs. the areas where academic freedom is strongly sanctioned.

For example, BYU offers its faculty and students free reign to explore the relationship between evolution and creationism, evidences of God/a higher power, the religious origins of morality, and the nearly supernatural insights/ideas/promptings that the Spirit provides. The academic community does not consider such topics to be scholarly; they are off-limits at nearly all non-religious universities, and secular professors that devote significant time to such topics will face a degree of persecution.

On the other hand, the professors, administrators, and students at BYU are not free to research and publish factual information about the Church (or past/present leaders of the church) that presents the LDS Church in a negative light. Doing so would put the individual's place at BYU in jeopardy (and could also bring sanctions that would be implemented at the ward level). At any other school, such criticism would be a non-issue.

This academic freedom issue hurts BYU both ways - they're intolerant of anything that opposes the LDS Church, and the areas where BYU does offer academic freedom are frowned upon by the academic community. BYU is a good school with a lot of good things going for it - but let's not kid ourselves. It's not an intellectually open institution, and - by the world's standards - it doesn't support academic freedom.