Scott Shane at the New York Times reports that “in more than six decades of fraught interaction between the agency and the news media, John Kiriakou is the first current or former C.I.A. officer to be convicted of disclosing classified information to a reporter.” Kiriakou succumbed to mounting legal bills and months of pressure from federal prosecutors by agreeing to a plea bargain under which he will serve thirty months for the crime of confirming to a reporter the identities of two former colleagues associated with the agency’s Bush-era extraordinary-renditions and torture programs: Deuce Martinez and Thomas Donahue Fletcher. The former was involved in harsh interrogations and later went to work with the principal architects of the CIA’s torture program, Bruce Jessen and James Elmer Mitchell. The latter was a principal coordinator of the extraordinary-renditions program. Shane’s report ably recounts the essential facts surrounding the Kiriakou case. It falls a bit short, however, in examining the broader policy issues raised by the case.

Here are the major questions, coupled with the answers suggested by the Justice Department’s management of the case:

(1) Who drives the prosecutorial decision-making in Espionage Act cases involving whistleblowers?

It seems clear, as has been suggested in several prior reports, that the Kiriakou prosecution sprang directly out of an investigation, launched by the CIA hierarchy, into efforts by Guantánamo defense counsel to probe the use of torture techniques on their clients. The CIA, fearing exposure of the identities of personnel involved in its torture programs, sought to use shield legislation (the Intelligence Identities Protection Act) to strike back against its critics, and to impose blinders on legal proceedings. Patrick Fitzgerald, the U.S. Attorney who oversaw the highest-profile and most successful prosecution involving the IIPA to date (that of Dick Cheney’s chief of staff, Scooter Libby), was tapped to handle this probe. Fitzgerald had credibility with the intelligence community, but he also appears to have been appropriately skeptical about the idea of using the IIPA to go after lawyers and organizations involved in the Guantánamo proceedings; ultimately, he departed the case. But the leads developed while Fitzgerald was managing the probe revealed Kiriakou to have been an important source for journalists covering Guantánamo. While Fitzgerald pushed back against the intelligence community, it does not appear that his successors at Justice had either the backbone or the will to do so.

Every year, Washington witnesses thousands of similar disclosures of classified information, prompting questions about who makes the call on when to prosecute cases, and about how these decisions are made. In the Kiriakou case, it is plain enough that whatever the formalities, the choices to open the investigation, to bring charges, and to pursue those charges aggressively were made not by the Department of Justice, but by the CIA. Former CIA general counsel John Rizzo has acknowledged that such requests regularly flow from his office, and that they reflect consultations with the CIA hierarchy.

During the Bush years, remarkably little evidence existed to show that Justice Department lawyers exercised independent judgment in matters surrounding torture and extraordinary-renditions programs. This relationship does not appear to have changed under Obama. Instead, the DOJ remains in the thrall of the intelligence community in general, and of the torture program’s architects and their protectors in particular.

(2) What provides the ratio decidendi for whistleblower prosecutions? Is there a corollary for cases involving torture?

DOJ spokespeople regularly tell us that thousands of breaches of secrecy take place in any given year. But only one or two of these cases actually leads to prosecution — so how are these cases selected? This is an important question, but one for which the DOJ has consistently failed to provide meaningful guidance beyond self-serving and generally inscrutable pronouncements about threats to national security.

Among their rationalizations is that such cases are difficult to prosecute. But Columbia scholar David Pozen demonstrated very persuasively in an important recent study of whistleblower prosecutions that this claim is false. Indeed, the Kiriakou case tends to support Pozen’s thesis, showing how easy it is for investigators to develop a case by subpoenaing a suspect’s phone and email records.

The Kiriakou case, like the Jeffrey Sterling and Thomas Drake cases before it, suggests strongly that DOJ prosecutors defer to senior figures in the intelligence community. These cases also indicate that those senior figures are permitted to target those who have embarrassed them by exposing incompetence, corruption, or criminal wrongdoing — the precise outcomes it is in the public interest to expose.

Kiriakou shows that protection of the authors and executors of the torture and extraordinary-renditions programs constitutes a particularly high national-security priority in the estimation of the intelligence community, and that this view is accepted and endorsed by the DOJ. In effect, the Espionage Act prosecution of Kiriakou amounts to a new DOJ torturer-protection program, designed to signal that the DOJ will intimidate those who give up information about people involved in torture.

It didn’t seem to matter in this case that Fletcher and Martinez’s identities were well known to persons investigating the torture program, and that Kiriakou’s confirmation of their names was hardly consequential. The prosecution of Kiriakou is confirmation of an official policy of omertà: those who rat on torturers and program masterminds will be treated ruthlessly.

(3) Should the IIPA be used to prosecute those who disclose the identities of operatives involved in the Bush-era torture and enforced-disappearance programs?

In the DOJ’s view, a covert-intelligence operative is entitled to the protections the IIPA is designed to preserve, so the exercise of the act is mechanical, and leaves no reason to probe whether its invocation is appropriate. But this points to the department’s misunderstanding or ignorance of the law governing torture and enforced disappearances. There is a commanding public interest in the disclosure of how these programs work and who is involved in them, and in the investigation and prosecution of related criminal acts. The use of the IIPA to thwart disclosure, investigation, and prosecution is not only perverse, it may itself constitute a criminal act of obstruction.

The real issue is not whether intelligence operatives are entitled to be protected from exposure because of the risk of criminal prosecution abroad. In fact, much of what covert operatives do in the course of their official duties (espionage, surreptitious entry, and wiretapping, for instance) may very well be criminal acts in the foreign jurisdictions in which they are acting. The IIPA may very reasonably be invoked to protect agents in such circumstances. But the situation is different when the criminal conduct rises to the level of a jus cogens crime — a rarified category of internationally recognized, universally enforced offenses that includes such crimes as slavery, torture, and enforced disappearances. In this case, the obligation to declare the conduct criminal, investigate, and prosecute it, is absolute. The United States has failed to discharge this obligation; in fact, the Attorney General has effectively flouted it by proclaiming a policy of impunity even for those guilty of torture-homicides.

It strikes me as quite implausible that the CIA fears that figures like Martinez or Fletcher will be targeted by terrorist organizations for their earlier actions. Rather, the Agency’s fear is very different: that covert operatives or former operatives will be sucked into pending criminal investigations into torture prisons, most notably a probe under way in Poland. It would indeed be surprising if Fletcher and Martinez were not already persons of interest in that investigation. Langley is likely also concerned about last month’s El Masri v. Macedonia ruling, which saw Europe’s highest court castigate Germany and Macedonia for failing to fully investigate and prosecute a team led by the head of the CIA’s international-jihad unit, Alfreda Frances Bikowski, involved in the sodomizing and torture of a German greengrocer in a horrendous case of mistaken identity.

The IIPA serves legitimate purposes, but the obstruction of pending criminal probes into torture and enforced disappearances is not among them. There is little doubt that this is the purpose the Kiriakou prosecution serves. The DOJ is claiming victory in the case when it should be ashamed. The prosecution raises fundamental questions about the department and its infamous role in American torture and enforced-disappearances programs, and demonstrates once more that the DOJ is aligning itself on the wrong side of the law — for torturers and against their victims; for deceivers and against the truth. To protect those involved in systematic torture and disappearances, the Justice Department is willing to put behind bars a decorated, dedicated intelligence officer, because he dared to speak the truth.