He was disparaging Obama, his "First do no harm" rules of engagement and the biggest idiot ever in Washington, VP Joe 7/11 Biden. I don't see that as a threat to civilian control.
I was talking to my son, who just returned from Afghanistan last month about this issue. His take was that McChrystal got a raw deal. Reporters over there make you think you can control what's on the record and off, but everything is really on the record. I'm sure McChrystal knew that, but the more junior officers probably made a few mistakes. That's why you ended up with the more "damning" quotes coming from "aides" and not much from McChrystal himself. Finally, they think he's a damned fine general and like him a lot. For my part, I think that he knew what he was doing. He let it out there on purpose and once it was out, he knew he would have to go. I don't think it would have been a good move on either part for him to attempt to remain in command. I know if I was McChrystal, I would not have gone back to Afghanistan under those circumstances, there would have been no way he could have commanded.