I remember when this first came out and it was as odd to hear about then as it is to read about it now. The church in general has guarded what you can say when representing any of its institutions.
I can see why BYU wants to maintain their respectability with the world, but I DO believe Prof. Jones' theory. He is only the most prominent member of the LDS church to believe that 9/11 was an inside job. Many, many people in the nation believe it also. Have you seen any of the programs in favor of the theory?
I attended a seminar featuring him at our local middle school. He told of how he was called in to meet with the heads of BYU. He said they asked him, "What's with all this conspiracy theory?" He said he replied with, "Not conspiracy theory, it is secret combination theory."
Since we know that secret combinations exist in the last days (now), who are working to overthrow the government through violence, and gain total control of it by subterfuge, is it too much to imagine that they would commit the atrocities of 9/11? Add to this doctrine the fact that the U.S. has a history of white flag operations to provoke wars, and what do you get? Plausibility.