WASHINGTON — The choice of Lt. Gen. Stanley McChrystal to become the new U.S. commander in Afghanistan has been hailed by Defense Secretary Robert Gates and national news media as ushering in a new unconventional approach to counterinsurgency.

But McChrystal’s background sends a very different message from the one claimed by Gates and the news media. His long specialization in counter-terrorism operations suggests an officer who is likely to have more interest in targeted killings than in the kind of politically sensitive counterinsurgency programs that the Obama administration has said it intends to carry out.

In announcing the extraordinary firing of Gen. David McKiernan and the nomination of McChrystal to replace him, Gates said that the mission in Afghanistan “requires new thinking and new approaches by our military leaders” and praised McChrystal for his “unique skill set in counterinsurgency”.

Media reporting on the choice of McChrystal simply echoed the Pentagon’s line. The Washington Post said his selection “marks the continued ascendancy of officers who have pressed for the use of counterinsurgency tactics, in Iraq and Afghanistan, that are markedly different from the Army’s traditional doctrine”.

The New York Times cited unnamed “Defense Department officials” in reporting, “His success in using intelligence and firepower to track and kill insurgents, and his training in unconventional warfare that emphasizes the need to protect the population, made him the best choice for the command in Afghanistan . . .”

The Wall Street Journal suggested that McChrystal was the kind of commander who would “fight the kind of complex counterinsurgency warfare” that Gates wants to see in Afghanistan, because his command of Special Operations forces in Iraq had involved “units that specialize in guerilla warfare, including the training of indigenous armies”.

But these explanations for the choice of McChrystal equate his command of the Special Operations forces with expertise on counterinsurgency, despite the fact that McChrystal spent his last five years as a commander of Special Operations forces focusing overwhelmingly on counter-terrorism operations, not on counterinsurgency.

Whereas counterinsurgency operations are aimed primarily at influencing the population and are primarily non-military, counter-terrorism operations are exclusively military and focus on targeting the “enemy”.

As commander of the Joint Special Operations Command (JSOC) from April 2003 to August 2008, he was preoccupied with pursuing high value al Qaeda targets and local and national insurgent leaders in Iraq, Afghanistan and Pakistan — mostly through targeted raids and airstrikes.

It was under McChrystal’s command, in fact, that JSOC shifted away from the very mission of training indigenous military units in counterinsurgency operations that had been a core mission of Special Operations Forces.

McChrystal spent an unusual five years as commander of JSOC, because he had become a close friend of then Secretary of Defence Donald Rumsfeld. Rumsfeld came to view JSOC as his counter to the covert operations capabilities of the CIA, which he hated and distrusted, and Rumsfeld used JSOC to capture or kill high value enemy leaders, including Saddam Hussein and al Qaeda’s top leader in Iraq, Abu Musab al-Zarqawi.

In 2005, JSOC’s parent command, the Special Operations Command (SOCOM), was directed by Rumsfeld to “plan, synchronize and, as directed, conduct global operations against terrorist networks in coordination with other combatant commanders”. That directive has generally been regarded as granting SOCOM the authority to carry out actions unilaterally anywhere on the globe.

Under that directive, McChyrstal and JSOC carried out targeted raids and other operations against suspected Taliban in Afghanistan that were not coordinated with the commander of other U.S. forces in the country. Gen. David Barno, the U.S. commander in Afghanistan, has said that he put a stop to targeted airstrikes in early 2004, but they resumed after he was replaced by McKiernan in 2005.

U.S. airstrikes which have caused hundreds of civilian deaths have become a major political issue in Afghanistan and the subject of official protests by Afghan President Hamid Karzai as well as by the lower house of the Afghan parliament. Many of the airstrikes and commando raids that have caused large-scale civilian deaths have involved Special Operations forces operating separately from the NATO command.

Special Operations forces under McChrystal’s command also engaged in raiding homes in search of Taliban suspects, angering villagers in Herat province to the point where they took up arms against the U.S. forces, according to a May 2007 story by Carlotta Gall and David E. Sanger of the New York Times.

After a series of raids by Special Operations forces in Afghanistan in late 2008 and early 2009 killed women and children, to mounting popular outrage, McChrystal’s successor as commander of JSOC, Vice Adm. William H. McRaven, ordered a temporary reduction in the rate of such commando raids in mid-February for two weeks.

However, the JSOC raids resumed at their original intensity in March. Later that month Gen. David Petraeus issued a directive putting all JSOC operations under McKiernan’s tactical command, but there has been no evidence that the change has curbed the raids by Special Operations Forces.

President Barack Obama’s National Security Adviser Gen. James Jones responded to Karzai’s demand for an end to U.S. airstrikes by saying, “We’re going to take a look at trying to make sure that we correct those things we can correct, but certainly to tie the hands of our commanders and say we’re not going to conduct air strikes, it would be imprudent,”

The airstrike in western Farah province that killed nearly 150 civilians last week, provoking protests by hundreds of university students in Kabul, was also ordered by Special Operations Forces.

McChrystal’s nomination to become director of the Joint Staff at the Pentagon in May 2008 was held up for months while the Senate Armed Services Committee investigated a pattern of abuse of detainees by military personnel under his command. Sixty-four service personnel assigned or attached to Special Operations units were disciplined for detainee abuse between early 2004 and the end of 2007.

Capt. Carolyn Wood, an operations officer with the 519th Military Intelligence Battalion, gave military investigators a sworn statement in 2004 in which she said she had drawn guidance for interrogation from a directive called “TF-121 IROE,” which had been given to the members of Task Force 121, a unit directly under JSOC.

However, the military refused to make that document public, despite requests from the American Civil Liberties Union and other human rights groups, protecting McChrystal from legal proceedings regarding his responsibility for detainee abuses.

He was never held accountable for those abuses, supposedly because of the secrecy of the operation of JSOC.

Although he has been linked with detainee abuses and raids that kill numbers of civilians, McChrystal has not had any direct experience with the non-military elements of such a strategy.

W. Patrick Lang, formerly the defense intelligence officer for the Middle East, suggested in his blog Monday that the McChrystal nomination “sounds like a paradigm shift in which Obama’s policy of destroying the leadership of al Qaeda in Afghanistan and Pakistan takes priority over everything else.”

The choice of McChrystal certainly appears to signal the administration’s readiness to continue Special Operations forces raids and airstrikes that are generating growing opposition by Afghans to the U.S. military presence.