To reiterate and highlight some key points made by previous posters:

1. McChrystal was relieved of his command for insubordination, not for "honesty."

2. "Sounding off in public, publicly attacking the policies or persons of the President, the Vice-President, the Secretary of Defense, etc., is in contravention of the military virtue of carrying out orders; it attacks the very constitutional structure of civilian-directed military procedure and discipline." AND IT IS IN VIOLATION OF THE MILITARY CODE OF JUSTICE. McChrystal could have been COURT-MARTIALED and perhaps should have been.

3. "Freedom Of Speech" means you cannot be prosecuted for expressing your opinions. It does not mean you can "speak" anywhere and at any time without consequences. And it does not apply within the US military, especially in the context of military operations.
The military does not operate by "reasoned debate" between superior officers and their underlings.

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McChrystal may have been deliberately seeking to be relieved of his command so he could retire and become a high-paid lobbyist or commentator. But apparently he had initially agreed to a 30-minute interview with the Rolling Stone reporter, and it was because of Skarpi's volcano (I know you don't control it, Skarpi, but it's in your back yard) that they were both stranded for several days. They ended up hanging around with each other for quite some time, drinking and trying to pass the lengthy delay time.   It appears that the extended "leisure" and alcohol consumption in the company of the RS reporter may have loosened McChrystal's lips and overruled his judgment.
He well might not have mouthed off so freely to someone he knew to be a reporter under other circumstances.

Of course, if this account is true, it begs the question of what other things might have slipped from his lips to who-knows-who-else under other circumstances of boredom, conviviality and strong drink.