So the scenario would be, not that the elders of the LDS church are secretly running the American intelligence community...

In fact, there are a lot of Mormons in the U.S. intelligence services. This isn't because of any sinister conspiracy,* but simply because of their institution of going off as missionaries to foreign countries. Most Americans, if raised speaking English in the home, have little motivation to properly learn another language, and don't. Mormons do -- they learn most of the languages of the globe and practice them under very trying conditions. Better yet, from the point of view of a government official concerned about security clearances, they do this without any family connections to the nations in question. BYU knows this.

• Of course, in your novel, you could say this is totally the result of a sinister conspiracy going back to Bringham Young. Dan Brown would approve.