[Never on my watch]

...generals are supposed to be apolitical...

Nobody is a apolitical...they should not sacrifice good military judgment to carry out poorly formed strategy. Speaking to Rolling Stone was probably not the best idea.

...They are not supposed to have political allegiance to the Pres.

Their allegiance needs to be the constitution. A lot of people sight to the fact that the President can give an unlawful order (as can anyone in the chain of command).

That said, I am not a fan of some of the decisions McChrystal has made (discouraging the use of flack jackets by our troops in civilian populations, for example).

[Yosemitest]

It's 20 pages from the "Air War College Air University",
but for anyone who really wants to understand this delicate quandary,
Please read Divided Loyalties: Civil-Military Relations at Risk.

... Consider the following instance of “necessary” and officially sanctioned lying.
Military members involved in highly sensitive, classified activities may be given a cover story that conceals the true nature of their work and told to adhere to it. If it’s legal to direct a member to disseminate a cover story--lie--in the interests of national security, is it also legal to order an officer to lie in the scenario’s circumstances?

The military oath, Constitution, and commissioning letter combine to form the legal basis of commitment and loyalty for military members. From these it is clear the superior loyalty should be expressed in protecting the values reflected in the Constitution. Additionally, the Uniformed Code of Military Justice (UCMJ) and Law of Armed Conflict contain legal considerations of which an officer should be cognizant. Sometimes, though, as in the scenario above, an officer is torn between two legitimate loyalties—the Army colonel legally owes loyalty to the Army Chief of Staff and President, but he also owes loyalty to the people (as represented by their elected members).

... The Air Force doesn’t mention the importance of loyalty at all in the publication that discusses its core values. It does, however, strongly advocate “faith in the system”:

To lose faith in the system is to adopt the view that you know better than those above you in the chain of command what should or should not be done. In other words, to lose faith in the system is to place self before service. Leaders can be very influential in this regard: if a leader resists the temptation to doubt “the system”, [sic] then subordinates may follow suit.

The implication is that an officer owes his or her ultimate loyalty to the system (the Service), rather than to the country or transcendent values. Officers are taught from the moment they first put on a uniform that loyalty to teammates is inviolable.

...COL (XXXXX) needs to tell the truth. Although he’s presented with two legitimate claims on his loyalty—loyalty to the Army and President versus loyalty to the Congress and the Constitution—expressing his loyalty to the former would require him to sacrifice his integrity and lie. Telling the truth is (XXXXX)’s best way of maintaining loyalty to himself, the Army, and the nation, even if it costs him his career. And as Colonel Charles Dunlap, Air Education and Training Command’s Judge Advocate General, points out,

“military people are expendable in a just cause. Disclosing information to legislators under the right circumstances, [as in the scenario], is simply part of the democratic process the U.S. military exists to defend.”

Sometimes an officer is called upon to sacrifice his comfort or career rather than his life. In our estimation, it’s an extremely rare instance in which an officer can sacrifice personal integrity and still make the right choice.