The Pakistani military intelligence service ISI received a lot of bad press in Pakistan in the aftermath of the successful U.S. raid against Osama bin Laden in the army-garrison town of Abbottabad. Like their Western counterparts, Pakistani journalists raised tough questions about whether ISI knew bin Laden was there or was simply too incompetent to find him. This blunt, rough questioning clearly stung the army-directed spy service, which is not used to being criticized in the mainstream Pakistani press. It has responded with strenuous denials and by suggesting, through intermediaries, that such criticisms are unpatriotic. But now there are accusations, publicly embraced by U.S. officials (including Joint Chiefs chairman Admiral Mike Mullen), that ISI ordered the murder of Pakistani journalist Saleem Shahzad, whose tortured and severely beaten body was found outside Islamabad on May 31.

Shahzad had recently written a piece for the Asia Times alleging that the Pakistani Navy had arrested several naval personnel for helping al-Qaeda attack the Pakistani naval base in Karachi on May 22. Suspicion that ISI may have been responsible for his death surfaced after it was revealed he had earlier told colleagues he had received death threats from the intelligence agency. These threats had allegedly come in the wake of a previous article he had written accusing Pakistani authorities of releasing Afghan Taliban deputy leader Mullah Baradar in October 2010 after eight months in custody. According to Shahzad, senior flag rank ISI officials had pressed him to reveal the source of his information and, when he refused, had made a point of telling him they had recently gotten a hold of an Islamic terrorist hit list and would let him know if his name was on it. Shahzad interpreted this as a threat. The speculation following his death was that the Karachi-naval-base story was the last straw and that ISI had ordered his murder, not just in retaliation, but as a warning to the entire Pakistani journalist community, whose criticisms it believed had gotten out of hand.

Well, maybe. ISI has a long history of intervening in political affairs at the behest of its army masters. When I served as the U.S. political counselor in Islamabad a decade ago it was conventional wisdom that ISI would “have a word” with individuals or groups whose activities it wished to deter. Some of my former senior-army-officer contacts even admitted as much. Interlocutors could range from radical Islamists, who would be encouraged not to carry out a planned demonstration or march, to unhelpful politicians, who would be confronted with dossiers detailing their corrupt and illegal activities. As far as physical coercion was concerned, this was much more the province of the considerably less disciplined and poorly trained civilian police and their political masters; it was Prime Minister Nawaz Sharif, for example, who had Najam Sethi, one of Pakistan’s leading journalists, beaten and carted off to jail for criticizing him in 1999. Interestingly enough, Pervez Musharraf, the army chief who overthrew Nawaz, proved to be signficantly more tolerant of press freedom than his predecessor.

If ISI was responsible for murdering Shahzad, it may well have been a first. The Committee to Protect Journalists reports that fifteen journalists have lost their lives in intentionally targeted killings in Pakistan since the murder of Daniel Pearl in early 2002, all of them Pakistani. Almost all were killed by radical Islamists affiliated with al-Qaeda or the Pakistani Taliban. The remainder were murdered for investigating regional ethnic conflicts or local corruption. None of the fifteen fit a plausible ISI scenario. But why would ISI choose Shahzad as its first victim? He was not a big-name journalist, nor was he among those who raised embarrassing questions about ISI and the army over the Abbottabad raid on bin Laden. His Karachi-naval-base story did not accuse ISI of improper conduct, and it is not clear why it would have killed him over a story that, if it embarrassed anyone, would have embarrassed the Pakistani Navy, a relatively minor player in the nation’s military firmament. ISI was well aware that some of its senior officers had recently “had a word” with Shahzad and should have realized that if he suddenly turned up murdered ISI might be blamed for it, further sullying its already battered reputation. And that, of course, is exactly what happened.

It probably deserves mentioning that others might have had a motive for killing Shahzad, including officers of the Pakistani Navy and members of al-Qaeda and its various Pakistani affiliates, although none have claimed responsibility. But the fact remains that senior U.S. officials told the New York Times they had “reliable and conclusive” intelligence that ISI was responsible. Admiral Mullen, in an interview late last week, was somewhat more circumspect, saying merely that the evidence showed Pakistani government—but not necessarily ISI—involvement in the killing. Whatever the intelligence involved, it must have come from either an intercept or a well-placed human source. It also seems to have been a fortuitous find, since discoveries of smoking guns directly implicating the notoriously secretive and careful Pakistani spy agency in various and sundry nefarious activities appear to be relatively rare events.

Also unexplained is why U.S. officials would reveal such information even if they were in possession of it. Relations between the CIA and the ISI have been seriously strained ever since CIA contractor Raymond Davis was arrested and detained last January for killing two Pakistanis he said were trying to rob him but who later turned out to be working for ISI. The Davis affair was followed just six weeks later by the raid on the bin Laden compound in Abbottabad, which poisoned relations even further. Needless to say, telling the New York Times there was conclusive evidence that ISI was responsible for killing a Pakistani journalist was unlikely to improve the relationship. The U.S. officials involved may have been motivated by human rights concerns, hoping to deter ISI from committing further such acts. But given recent events, there could also be elements of bad blood at work here.

Just two days after Admiral Mullen made his accusations on the Shahzad murder, the New York Times revealed the United States was suspending military assistance to Pakistan. Washington has been increasingly frustrated at Islamabad’s unwillingness to go after those Afghan Taliban forces using the North Waziristan tribal area as a safe haven for conducting operations in eastern Afghanistan. The Pakistanis have refused to do so because they see the Afghan Taliban as a hedge against the emergence of a hostile government in Kabul allied to India after U.S. forces depart the region. Although little publicized in the West, the Indians have developed close ties to the Karzai government, flooded the country with aid workers and provided the Afghans with over a billion dollars in aid. Although the Pakistanis have no particular love for the Afghan Taliban—whose support for Osama bin Laden got them into their current fix—they fear the Indian presence in Afghanistan even more. Not only has the United States shown little sympathy for these Pakistani concerns, it has grown increasingly angry at Pakistani reluctance to do what it wants. Seen in this context, the U.S. decision to publicly accuse ISI of complicity in the Shahzad murder can be viewed as just another manifestation of American displeasure.

Given the strength of Pakistani concerns about Afghanistan, however, there may be no amount of pressure capable of forcing the Pakistani Army into going after the Afghan Taliban. If anything, U.S. pressure to date has only served to fan the flames of anti-Americanism both among ordinary Pakistanis and within the army. The danger is that, by continuing to ratchet up the pressure, Washington may provoke a final break with the Pakistanis. This would not only jeopardize the U.S. ability to supply its forces in Afghanistan, which rely heavily on land routes through Pakistani territory, but could lead both sides down the slippery slope to a shooting war. The Pakistani Army is already engaged in a protracted, bloody struggle against hostile Pakistani Taliban forces in the tribal areas and is widely regarded as the only force in the country capable of preventing a jihadist takeover of the government. While the current situation is certainly a mess—and U.S. frustrations are understandable—things could very easily get a whole lot worse.