When Civilians Work Against National Security

From News Dissector blog:

I asked retired Air Force Colonel Sam Gardiner for his take on Zarqawi. He is an expert on information warfare and appears in my film, WMD:

"1. The US made more of him than he was. We made more of his connection to Osama bin Laden than there was. We will make more of his killing than there is.

"2. Last week, I was a guest on Alhurra TV, the Washington-based television network sponsored by the USG to counter Aljazerra. The anchor asked my why the US bombed the house rather than attempting to capture the individuals there. I could not answer his question. I could only say I wish we had not done it the way we did. I'm very uneasy by the growing parallels between the US response and the Israeli response, standoff assassination."

I agree with this Colonel and probably a fair few of the military officers that have anything to do with Iraq?

Isn't there some kind of idea that the military's best interest is to wage war? That we have a civilian as a Commander in Chief to prevent wars that don't have a good reason?

Who acts as the check to the Commander in Chief when he wages a war against the nation's security?