I think there is a lot of oversimplification. If you are an Islamofascist, why wouldn't you try to ingratiate yourself to the intelligence agencies and only feed them what you want?
One of the disadvantages to a civilian run military. Which is one of the BIG reasons why it's important to limit the scope of the Federal Government. It's putting a lot of power in a position that has a high turnover rate and no oversight. Typically not the best idea.
I take that back, the IG is supposed to provide oversight, but often they are not informed of everything that is going on, and are frequently impeded in their investigations.
Now homegrown Anwar Al-Awlaki is the boogeyman that we will chase around and give us a reason to bomb more countries and continue our never-ending war.