You make a very reasoned argument, however I don’t think the General is dealing with a reasonable individual. I think the General is doing what he thinks gives the men and women under his command their best chance for success.
Duty, honor, and country means that you tell the truth and do what is right for your people and your nation. We either get out of Afghanistan or win. If I were McCrystal, I would resign and then speak out against a policy that endangers my people and the mission. He can not do that now because he is part of the chain of command starting with the CIC.