From our country's earliest beginnings, the founding fathers knew the potential hazard of this or any country being taken over by a stratocracy -- a military dictatorship. To minimize that potential, they drafted, as part of our Constitution (Article 1 section 8), a specific structure that clearly positions the military under the direction of the Executive Branch of the Government and with their funding being controlled by Congress. Thus, their power is balanced between the two most prominent civilian legislative branches of government.
While it is important that we don't have a lap-dog military that can't express any concerns over the commands that they may receive from the Executive Branch, it is also important that they maintain a certain level of respect for the civilian leadership that they report to. That's because any erosion of that respect might actually create a situation whereby the military becomes autonomous to some degree; with the worst case resulting in some kind of coup.
The McChrystal situation presented a real conundrum because he is the primary architect of the military plan that is only half-way implemented in Afghanistan and prior to the draw down of troops starting next year. To lose him over his disrespectful comments may actually jeopardize the results of the war.
One option that was available to Obama was to elicit a public apology from McChrystal (assuming he's sorry). Then, bust him down by one or two stars from his four-star status and allow him to continue in his role as the Afghanistan commander. However, this ignores the fact that there might be a serious dissenting attitude in his command and below towards our civilian government.
I think the only real option for Obama was to have accepted McChrystal's resignation. He probably should have been stripped of some of his rank to show how serious an offense he had committed. For the protection of the precepts of our Constitution with regard to the military, Obama absolutely had no other option.
Our country has, probably, the best military in the world. No one man is irreplaceable. There are a lot of people in the ranks who could replace McChrystal and continue the plan in Afghanistan. Certainly, the replacement of McChrystal with Petraeus was a good choice but it might have just left Iraq exposed. In addition, Obama needs to strengthen his leadership skills so that this kind of disrespect doesn't fester once again. And, too, if we continue to see unrest in the military over the Administration's leadership, it is the people of this country who will need to reprimand Obama for his actions.