The elected civilian leadership has, and must always have, full, complete and unquestioned control over the military. That's obvious; it's a fundamental part of democracy.
How the control is applied, however, is or ought to be a matter for deliberation and calibrated calculation. Just as Israel was right to block that flotilla but not smart about it, to give a recent example. There's usually more than one way to do things, and this goes for the relationship between elected civilians and appointed generals as much as it's true about anything else.
The narrative is that everyone, left to right, agreed that McChrystal had to go: you can't have a general bad-mouthing the elected leaders (though why saying that Obama was uncomfortable at an early meeting with the generals is bad-mouthing, is beyond me. It was an observation, probably an accurate one, and not denigrating in any way I can see). According to the New York Times, however, this isn't so: there was a fierce argument about balancing the need to discipline the general and the possible damage to the war effort.
But it was a short argument:
The press secretary, Robert Gibbs, walked a copy of it to the president in the private quarters. After scanning the first few paragraphs — a sarcastic, profanity-laced description of General McChrystal’s disgust at having to dine with a French minister to brief him about the war — Mr. Obama had read enough, a senior administration official said. He ordered his political and national security aides to convene immediately in the Oval Office.George Patton, anyone?
I read the Rolling Stone article. There was bad-mouthing in it, and jack-assing, if there is such a word. The general and his staff come off as top-notch soldiers and poor politicians, though McChrystal's relationship with Afghanistan's President Karzai indicates he's not a bad diplomat when he feels it's essential to his mission. I didn't see any insubordination, and certainly no threat to democracy. Sorry: I didn't.
But as I say, this may be a cultural thing. As I've repeatedly explained in the past, Israelis use words differently than Americans. Very differently. This isn't to say there's a right way or a wrong way. My feeling after reading the article was that Obama should have pulled in the general, given him a severe tongue-lashing, the general should have submitted his resignation, and the president should have glared at him and said "Are you kidding? You've got a job to do! Now go back and do it, and I don't want any more of this behaviour from you ever again. Dismissed".
It's not true there's no-one who can't be replaced. Sometimes, removing a key figure at a crucial moment results in significantly different outcomes. Were this not so, we'd never try so hard to replace/retain political leaders whom we feel strongly about, for example.
I, for one, am uncomfortable that there's such a broad consensus in an America at war that careless words so obviously trump carefully-planned actions. This may reflect an Israeli feeling that blunt words are better than civil ones, since they're closer to the truth; it may reflect a lifetime of living near or at real war, an experience most Americans, fortunately for them, don't have.
Barry Rubin, another Israeli who writes often in English, thinks the real problem is that McChrystal's words were mostly true.