IMO, even as the offense is one for which a military officer could be fired, perhaps the best course would be for the President to bar General McChrystal from any contact with the media. Instead, a separate military officer should be designated to handle press matters, with neither General McChrystal nor his staff having any media contact. Their contact with the media officer should be limited to providing requested facts/information. Framing the message would be outside General McChrystal's and his staff's purview. Although the General would likely resist such constraints, his now repeated damaging public relations blunders have demonstrated an inability to handle the media. If he rejects such terms, then he should be relieved.
However, for even the above framework to be feasible, others including Amb. Eikenberry, Richard Holbrooke, and General Petraeus would need to have sufficient confidence that they could work with General McChrystal. The effort in Afghanistan is a team effort. If the General's comments have destroyed the ability for the group to function as a cohesive team, then a replacement will be needed.
With Congressional criticism of the General's conduct increasing, and criticism has been expressed by Rep. Obey, Sen. McCain, and Sen. Kerry, among others, the President will need to consider the political dynamics. If Congress has lost confidence in General McChrystal, it also makes little sense to retain him.
Finally, if the President chooses to retain General McChrystal, he should reaffirm that he expects that the strategic objectives set forth in the strategy largely designed by General McChrystal will be fulfilled by the time July 2011 arrives. The situation might also present an opportunity for the President to suggest corrections to the strategy e.g., reducing its current Kabul-centric focus.
Right now, my guess is that the President could go either way on the issue. A lot will depend on whether the Afghanistan "team" can function effectively or whether the General's comments have destroyed the necessary trust and relationships. Congressional pressure will be another factor. General McChrystal might tender his own resignation, which I suspect the President would accept if it is offered.