"1) Reasoned debate and free speech no longer exist in America when it doesn't suit the 'national interest'"
You're saying that this is a free speech issue?...That free speech is allowing a reporter to follow you around for weeks as you and your staff snipe at your commander in chief?
Free speech is what allows the Rolling Stone to publish the article; and you and I to discuss it. There won't be a phalanx of government agents smashing the Rolling Stone presses, or shooting the reporter in the night, or threatening his family.
The fact that the General chose to be insubordinate and allowed his staff the same on the record shows poor judgment. Any officer in the US military know that they lose the right that civilians enjoy to make public statements about the chain of command when they sign up. That right is returned to them when they retire or leave the military.
If the general's resignation is accepted by the president, McChrystal will be free to make his case on Fox news, or MSNBC, or CNN or any other news outlet of his choice...or not.

"Your' Commander in Chief' was in short pants when McChrystal started out.' That may be. I don't know if President Obama ever wore short pants; but he IS the Commander in Chief right now. That means that he the general's boss...period. The same was true when George Bush was the president and made questionable choices.