It is not about Afghanistan policy -- although, of course it's about that too, with McChrystal as the face and mind of the strategy Obama bought into at the end of last year.
It's about civilian control of the military, respect for the chain of command, and the concepts of disrespect and insubordination. Every officer and enlisted person in every military branch is well schooled in what those concepts mean.
If the facts are as they appear -- McChrystal and his associates freely mocking their commander in chief and his possible successor (ie, Biden) and the relevant State Department officials (Holbrooke and Eikenberry) -- with no contention that the quotes were invented or misconstrued, then Obama owes it to past and future presidents to draw the line and say: this is not tolerable. You must go. McChrystal's team was inexplicably reckless in talking before a reporter this way, but that's a separate question. The fact is -- or appears to be -- that they did it
The second step is what this means for US strategy in Afghanistan, the future of COIN, etc. But the first is for the civilian Commander in Chief to act in accordance with Article II, Section 2 of the Constitution and demonstrate that there are consequences for showing open disrespect for the chain of command.
And, yes, I would say the same thing in opposite political circumstances -- if, for instance, a commander of Iraq operations had been quoted openly mocking George W. Bush and Dick Cheney. Resign in protest: yes, a course of honor. But protest and mock while in uniform, no.