Ok, Here's one piece of evidence that totally debunks this entire idea.
Planes burn. Missiles explode.
But, if that wasn't convincing enough, do some research on to what the construction of that piece of the pentagon actually consisted of. There is a great poster in my ARCHITECTURAL ENGINEERING DEPARTMENT IN PENN STATE that tells you exactly how, and why the building did what it did. That also includes the windows.
But what would they know? They only design, build, and fix the friggin things. Quite literally. One of my professors helped design the windows to withstand impacts quite like the one that happened on 9/11.