On this matter of newspapers printing information about secret government programs, the best article I've read — or at least, the one I most agree with — is this piece by Glenn Greenwald. As usual, government officials are screaming "it's anti-American" whenever the press refuses to spin the news their way.
I would also call your attention to an article by Matt Yglesias. It basically says that no matter how much you think the "Global War on Terror" is costing us in terms of dollars, your estimate is way low.