I read the notorious Rolling Stone article about Gen McCrystal and Afghanistan. I'm not entirely clear on what Obama finds so objectionable. I didn't see any quotes or reporters opinions disrespectful of the President. I did see a long article disparaging the war, casting doubt on the chance of victory, emphasizing internal friction, badmouthing the Afghans, all in all a downer of an article. The kind of hatchet job that Seymour Hersh used to do for the New Yorker. The author also paints McCrystal in an unflattering light. In fact, the article makes McCrystal look way way worse than it does Obama and the administration.
Clearly McCrystal allowed the wrong reporter access to Afghanistan and even granted him interviews. Surprising. We in the military learned not to trust the US press back in Viet Nam. I guess McCrystal forgot, or maybe never learned, that US reporters will write stories that make you personally look bad and discredit your unit and your branch of the service.
Of course, it could be that Obama, impatient for progress, has decided it's time for a better commander in Afghanistan, and the Rolling Stone article is a convenient excuse.