People debate over and over about just what exactly the principle of 'academic freedom' entails. But, I think it's fairly simple actually. Should a professor or instructor be allowed to hold an unpopular view? Yes. The university administration has no right to dictate what views their employees hold in their personal life. Just as a professor has no right to dictate what views their students should hold.
And so, the professor has the right to believe that aliens have visited Earth, but he or she does not have to the right to propose this idea to their students as gospel truth and require them to agree to it for a grade, or even to imply such a requirement. In fact, the idea of 'gospel truth' is largely anathema to higher ed. In matters of opinion, we have the responsibility to present opinions, if we choose so, as opinions. That's it. We're not required to avoid all controversial opinions- nothing is verboten in a marketplace of ideas. But, we are required to keep all opinions, especially our own, under an unblinking lens of skepticism.
So, Brigham Young University seems to be out of their tree in suspending Dr. Steven Jones for holding the opinion that the 9/11 attacks were an 'inside job'. Whether or not he's right, and my cursory review of the State Department report and his own website leads me to believe the latter, is not what should decide his employment. In fact, his personal opinions, again, are not the property of the university. Did he present his opinions in a classroom as proven fact? It doesn't even sound like he mentioned them in class from the article.
BYU is not a good place to teach, clearly. They've fired other instructors for such petty infractions as writing letters to the editor of the local paper in support of gay marriage. And generally they seem to take the attitude that 'if you work here, you'll believe what we tell you to believe'. Such an attitude is poisonous to intellectual freedom.