The traditional view of these matters, the idea of objective civilian control, says that this is a political decision that officers should not publicly consider, as doing so will politicize the military. But what exactly is the grave harm we fear here? A coup? A collapse of command authority? These are impossible and far-fetched, respectively. I doubt politicized generals are going to poison debate, and they might even improve it. For example, it would have been helpful if more generals publicly knocked the light footprint Rumsfeld wanted for the invasion of Iraq.
A bigger danger from comments like McChrystal’s is that they damage the Army’s apolitical reputation. But since that reputation is somewhat fictional the top layers of the military are plenty political I don’t know if that’s a bad thing. A realist’s view of this matter is that McChrystal can express his views and the President can always fire him, if he can bear the political cost.