But wouldn't that lead to a "scandal" because the CFI would then over step it's bounds? And people would be screaming for Bush's head because he interfered in how the law said things should be done (say for instance the CFI approves the economic part of it and the FBI or CIA approves the terrorist threat part of it).

I think you and I both know that "securing America's interest" reason for Bush doing that would be thrown out the window in hopes of getting him impeached or smearing his name even more.