The Pentagon’s exoneration of Gen. Stanley McChrystal in connection with remarks attributed to him and his staff in a magazine article last year points to continuing civilian-military tensions and raises the question of why he was really fired from his post as senior US commander in Afghanistan.

According to the Department of Defense inspector general’s report, which was obtained under the Freedom of Information Act and reported Monday by the New York Times, “The evidence was insufficient to substantiate a violation of applicable DoD standards with respect to any of the incidents on which we focused.”

The most serious of these violations concerned Article 88 of the Uniform Code of Military Justice, known as the “contempt toward officials” offense. The article, which prohibits uniformed officers from using “contemptuous words” against the president of the United States and other top civilian officials, is meant to buttress the increasingly tattered principle of civilian control over the military.

The article, which appeared in Rolling Stone magazine in June 2010, quoted McChrystal and senior members of his staff making contemptuous remarks relating to President Barack Obama, Vice President Joe Biden and other senior administration officials.

McChrystal was quoted in the article as stating, “Are you asking me about Vice President Biden? Who’s that?” To which an aide is said to have retorted, “Biden? Did you say ‘Bite me.’”

It also quoted a McChrystal aide as referring to Obama’s then-national security adviser Gen. James Jones (ret.) as a “clown,” and McChrystal himself describing Obama as “uncomfortable and intimidated” by the presence of top military brass in the White House.

In its general conclusions, the inspector general’s memorandum states, “Not all of the events at issue occurred as reported in the article. In some instances, we found no witnesses who acknowledged making or hearing the comments as reported. In other instances, we confirmed that the general substance of an incident at issue occurred, but not in the exact context described in the article.”

However, in dealing with particulars, the memorandum substantiates the derisive banter in relation to Biden and expands upon it.

It states, “We consider credible a witness’ recollection that Gen. McChrystal said, “Are you asking me about Vice President Biden? Who’s that?” and that a follow-up comment or rejoinder of some sort referring to Vice President Biden was made…and that rejoinder may have included the words ‘bite me.’” The document adds that the investigation was “unable to establish the exact words used or the speaker.”

The report adds that McChrystal’s staff referred to any potentially problematic questions that the general might receive in response to public speeches as “Biden questions.” This was a reference to the internal divisions within the Obama administration between those who favored the “surge” that sent another 30,000 US troops into Afghanistan and others, including Biden, who supported a “counter-terrorism” strategy that would have reduced troop numbers and relied more heavily on drone missile attacks and special forces operations to assassinate suspected leaders and members of the armed groups opposing the US-led occupation.

McChrystal had publicly attacked Biden’s position in a 2009 speech he delivered before a military think tank in London, in which he all but demanded that the American president send in the additional troops he had recommended.

As to the remark dismissing the US national security adviser as a “clown,” the memorandum said, in a phrase that is repeated in more or less identical form throughout the document, “We were unable to verify that this comment was made, and, if it was made, by whom.”

Rolling Stone posted a statement on its website defending the accuracy of the reporting by its correspondent, Michael Hastings.

“The report by the Pentagon’s inspector general offers no credible source―or indeed, any source―contradicting the facts as reported in our story,” it said. “Much of the report, in fact, confirms our reporting, noting only that the Pentagon was unable to find witnesses ‘who acknowledge making or hearing the comments as reported.’ This is not surprising, given that the civilian and military advisers questioned by the Pentagon knew that their careers were on the line if they admitted to making such comments.”

The report’s conclusion that the evidence did not substantiate charges that McChrystal had violated Pentagon standards amounted to a direct contradiction of Obama’s explanation last year for his firing of the Afghanistan commander, in which he accused him of falling short of “the standard that should be set by a commanding general.”

McChrystal retired from the military late last year, his career effectively ended by the loss of his command in Afghanistan.

The Pentagon memorandum was issued on April 8, four days prior to the Obama administration naming McChrystal to co-chair a new advisory commission concerned with the welfare of military families. Giving the timing, there is speculation in Washington that the appointment was meant to deflect rancor over McChrystal’s firing within the officer corps, and particularly within the special operations command, which he previously headed.

A report in the Wall Street Journal suggested that bestowing the largely ceremonial post has not had the desired effect.

“Some defense officials portrayed the report by the Pentagon inspector general as a vindication of Gen. McChrystal,” the paper reported. “Still others, who viewed the general’s ouster as misguided and unfair, found any sort of seeming exoneration to be bittersweet.”

The appointment has also been overshadowed by its condemnation by Mary Tillman, the mother of Pat Tillman, the former NFL player who left his career in professional football to become an Army Ranger and was killed in Afghanistan.

McChrystal, then the commander of all special operations forces, knew that Pat Tillman had been killed by his fellow soldiers in what has been described as an accident, or case of “friendly fire.” Nonetheless, he led a cover-up of the incident, promoting a propaganda campaign that portrayed Tillman as a hero who had been killed by the enemy.

While a Pentagon inspector general recommended that McChrystal face disciplinary action for lying to the family and to the American people, the Pentagon failed to pursue the matter.

Mary Tillman described the appointment as “a slap in the face to all soldiers.”

McChrystal had hardly been banished to obscurity after his firing. Like many newly retired top officers, he quickly landed himself a position with a major weapons contractor, being appointed in February to the board of directors of Navistar, a top supplier of armored vehicles to the US military. He is also a regular on the corporate lecture circuit.

Not surprisingly, sections of the Republican right are using the Pentagon report as a political weapon against Obama. Rupert Murdoch’s tabloid, the New York Post, published an editorial entitled “McChrystal restored,” condemning the firing and defending the expression within the military of hostility toward the civilian government.

“Soldiers being soldiers―and Team Obama being totally feckless regarding military matters―it seems likely that some remarks unflattering to the administration were uttered,” the editorial acknowledges approvingly.

There is no doubt that the kind of statements attributed to McChrystal and his staff reflect views that are widespread within an officer corps that has grown increasingly politicized along right-wing, Republican and Christian fundamentalist lines, while given unprecedented powers as it wages an unending and global “war on terrorism.”

The reality, however, is that a substantial layer in the Republican Party supported McChrystal’s removal, not out of any concern for his derogatory remarks toward Obama, Biden and Co., which served only as a useful pretext.

Rather, they backed a change in the command of the nearly decade-old Afghanistan war out of concern that it was turning into a debacle, with the successes that McChrystal had predicted for the “surge” wholly unrealized. The controversy over the Rolling Stone article surfaced as it was becoming painfully clear that a much-vaunted offensive in the Marjah region of Helmand Province had failed to rout the Taliban, and the counterinsurgency doctrine of “clear, hold and build” was failing even in the “clear” stage.

McChrystal’s implementation of the counterinsurgency strategy that was drafted in large part by his successor, Gen. David Petraeus, was blamed for the deepening quagmire. In particular, his critics, both within the political establishment and sections of the military, condemned his orders to limit the use of air strikes in an attempt to bring down civilian casualties, which are seen as one of the main grievances fueling Afghan resistance to the US occupation.

Shortly after assuming command in Afghanistan, Petraeus reversed this policy, and the number of air strikes now being carried out by US warplanes is nearly double what it was a year ago.

Wholesale violence on the ground has also characterized the ongoing offensive in Kandahar, as a Washington Post article quoting the Pentagon’s claims of “security improvements” in Kandahar made clear.

“The security improvements have been the result of intense fighting and the use of high-impact weapons systems not normally associated with the protect-the-population counterinsurgency mission,” it states. It describes US units “flattening” and “razing” villages with air strikes and artillery.

Whatever temporary effect these brutal methods have on armed resistance in the area, Petraeus has had no more success than McChrystal in producing any sustainable pacification of Afghanistan. The US operations in Kandahar have been accompanied by a spread of armed resistance throughout the rest of the country, and the US-trained Afghan security forces have proven incapable of playing the role designated for them by Washington of holding what the American military “clears.”