Setting aside whether that's true, there is still the UCMJ. The what? you ask. The Uniform Code of Military Justice which makes clear that uniformed military personnel cannot criticize the President of the United States, and among many military in Afghanistan it was a topic of conversation.
Meanwhile, the concern about the media and the military's relationship is on the mind of Gen. McChrystal's successor (and this comes from the Wall Street Journal) --
'Pentagon officials are concerned the military may recoil in fear and anger from the press. The chill couldn't come at a more inopportune time for the Pentagon's leadership, with skepticism about the war's progress growing among U.S. politicians and officials in Afghanistan ahead of what is likely to be the war's most important operation, the imminent move by thousands of U.S. forces into Kandahar, the spiritual heartland of the Taliban. 'If we recoil, if we go underground, if we get defensive, it's self-defeating,' said Geoff Morrell, the Pentagon press secretary. 'We need to remain as engaged as ever, if not more so because we are at a crucial point in this war.' ... Gen. Petraeus is expected to seek to keep the command relatively open, a policy he instituted as commander in Iraq.'
Let's acknowledge the root of this story -- the general's words and actions. Don't let the "yes, but" comments get in the way.