It's easy to see how the President would feel tempted to accept it, under the auspices of reasserting civilian control of the military. There's no doubt that the General exercised terrible judgment, and it's completely understandable if the President were both angry and disgusted.
But here's the thing: This isn't about the President and his feelings. This is about the success of America's mission in Afghanistan. If he believes that McChrystal is the best man for completing the mission, the President has a duty to retain him, notwithstanding his unfortunate behavior.
Let's think of it this way. The President has had no problem eating humble pie on behalf of America, with repeated apology tours in pursuit of what he apparently believes is a better foreign policy for this country. If he's willing to allow America to eat humble pie in service to the "greater good" (by his lights), shouldn't he demonstrate the same willingness, on a personal level, to swallow his personal pride? If Iran and North Korea and Venezuela and others can flip America the bird -- and America is supposed to sit back and accept the criticisms with introspection and humility -- shouldn't the President model the kind of behavior he demands collectively from his fellow citizens?
Of course, but don't count on it happening. The one time the President ever shows real anger has nothing to do with attempted terrorist attacks or spewing oil wells. It's when someone criticizes him. McChrystal (and/or his staff) has committed that mortal sin, so it's obvious the General is not long for his job.