The most prominent concern hyped by the United States government and the establishment media after WikiLeaks published the Afghanistan War Logs was that the military incident reports endangered the lives of U.S. soldiers and Afghan informants. But an email released in the last batch of State Department emails from Hillary Clinton’s private server suggests something else entirely was of bigger concern.

Over 90,000 military incident reports were provided to WikiLeaks by Chelsea Manning, who is now serving a 35-year sentence in Fort Leavenworth after being convicted of Espionage Act-related offenses.

An “executive summary” [PDF] on the “WikiLeaks release of Afghanistan/Pakistan-related documents” from the Office of the Assistant Secretary of Defense for Public Affairs focuses attention on how the Afghanistan war logs negatively portrayed U.S.-Pakistani relations. It was dated July 23, two days before the war logs were published.

“Representatives of the NYT [New York Times] have described to USG [U.S. government] officials the nature of some documents as casting U.S.-Pakistani relations in an unfavorable light, particularly with respect to the ISI,” which is the Pakistan government’s domestic security agency.

It continues, “The ISI is allegedly described as continuing to support AQ, the Haqqani network, and Taliban (Quetta Shura) in opposition to U.S. and Afghan interests. The documents allegedly do not provide ‘blockbuster revelations’ but instead present a richness of detail previously not known or released and a damning portrait of U.S.-Pakistani relations sustained over several years.”

“The documents related to Afghanistan portray day-to-day activities there through combat operations, incidents, and accidents and casualty events, both civilian and military,” the summary adds.

At first, the Pentagon did not claim the documents would pose a risk to any lives. David Lapan, deputy assistant secretary of defense for media operations—from the same department which prepared this executive summary, told NBC News’ Michael Isikoff that none of the documents reviewed so far carried a classification level above “secret,” which is the “lowest category of intelligence material in terms of sensitivity.”

Lapan changed his tune less than twenty-four hours later. “We will be looking at [the documents] to try to determine the potential damage to lives of our service members and our coalition partners, whether they reveal sources and methods and any potential damage to national security,” Lapan said to Reuters. “It will take a matter of days, if not weeks, again depending on how these documents are actually made available so that they can be reviewed.”

Was this decision to focus on potential lives at risk an effort to deflect attention away from the issue of U.S. and Pakistan relations and how they were impacting the Afghanistan War?

Pentagon spokesperson Geoff Morrell said on August 11, 2010, “We have yet to see any harm come to anyone in Afghanistan that we can directly tie to exposure in the WikiLeaks documents.” Secretary of Defense Robert Gates’ suggested days after the release, “There has not been a single case of Afghans needing protection or to be moved because of the leak.” The Associated Press concluded on August 17, “There is no evidence that any Afghans named in the leaked documents as defectors or informants from the Taliban insurgency have been harmed in retaliation.”

However, White House Press Secretary Robert Gibbs claimed, “I don’t think that what is being reported hasn’t in many ways been publicly discussed, either by you all or by representatives of the U.S. government, for quite some time,” and went on to discuss how the press was fully aware of how Pakistan may have “safe havens” that were aiding the Taliban and the White House had been making progress in addressing this problem.

But then, why was the public affairs arm of the Pentagon concerned in the “executive summary” about what the war logs showed in relation to Pakistan?

Part of the proposed “actions” in response is redacted. But most of the paragraph is in tact in the email that was released.

“Talking points are being developed for use in response to query once news stories begin to appear,” the summary declares. “The statements and RTQ [responses to queries] will strongly condemn the transfer of classified information to persons not authorized to receive it and publication by various organizations that could cause harm to U.S. service members and national security.”

“The products will highlight the new, integrated Afghanistan-Pakistan strategy implemented over the past six months and the differences in Afghanistan and Pakistan in 2010 compared to [the] period covered by the documents,” the summary additionally indicates.

Notably, there is nothing in the uncensored portion about going through the documents to figure out whose lives were endangered. It is possible this is what the sentence withheld addresses. In fact, a separate email [PDF] notes the Defense Department will review the documents, and part of that sentence is redacted. But it is public knowledge the Pentagon planned to conduct a review of the documents to see who was in danger as a result of publication.

The assessment of the publication, according to the summary, was that “release of the documents and media reporting on them” would “likely provoke negative public reactions in Pakistan and Afghanistan.” There would also be “significant, but less volatile, public, and government reaction in the U.S. and Europe.” Again, there’s nothing about risks to troops or “informants” as hyped by media and even human rights organizations.

Finally, the coordination between the Times and the government over the WikiLeaks disclosures has received quite a bit of attention. The coordination offered the White House the opportunity to circulate a file that featured many of the president’s and the administration’s leaders’ remarks on the role of Pakistan in the Afghanistan War. It made it possible to tamp down scrutiny from the press before there was anything published to scrutinize.

This summary further demonstrates how the Times advised the government on what in the documents would be damning to the Obama administration. It was the Times’ calculation that the reports relating to Pakistan were the most newsworthy. On the other hand, what is significant is the “executive summary” appears to quote the Times when claiming there are no “blockbuster” revelations.

Both the Times and the government were wrong. Even if the revelations did not have the impact of ending the Afghanistan War and pushing officials to hold officers accountable for war crimes, Der Spiegel‘s coverage highlighted “Task Force 373,” an assassination squad comprised of Navy Seals and members of the Delta Force which kept classified lists of “enemies.”

On June 17, 2007, a mission was undertaken to kill “prominent al-Qaida functionary Abu Laith al-Libi.” The squad staked out a “Koran school where he was believed to be located for several days.” An attack was ordered. The squad ended up killing seven children with five American rockets. Al-Libi was not killed.

Days before this failed assassination attempt, according to coverage by Nick Davies of The Guardian, the squad “set out with Afghan special forces to capture or kill a Taliban commander named Qarl Ur-Rahman in a valley near Jalalabad. As they approached the target in the darkness, somebody shone a torch on them.” There was a firefight. An AC-130 gunship was called in to fire its cannon and clear the area. The squad discovered “the people they had been shooting in the dark were Afghan police officers, seven of whom were now dead and four wounded.”

On October 4, 2007, the squad confronted Taliban fighters and then called in air support to drop five hundred pound bombs. The carnage that resulted included: “12 US wounded, two teenage girls and a 10-year-old boy wounded, one girl killed, one woman killed, four civilian men killed, one donkey killed, one dog killed, several chickens killed, no enemy killed, no enemy wounded, no enemy detained.”

As Manning declared during her trial, “In attempting to conduct counterterrorism and counter-insurgency operations, we became obsessed with capturing and killing human targets on lists, on being suspicious of and avoiding cooperation with our host-nation partners, and ignoring the second and third order effects of accomplishing short-term goals and missions.”

The Afghanistan War Logs offered a glimpse at how the U.S. government embraced the policy of targeted assassinations in military operations. The operations detailed were precursors to the rise of drone operations, where hundreds if not thousands of innocent civilians would be killed in the war and in Pakistan, away from the battlefield.