Whatever the outcome of a case, then-Attorney General Robert H. Jackson observed in 1940, “the government .... has really won if justice has been done.” It’s worth keeping that truth in mind as we consider the dispute over Attorney General William Barr and Roger Stone.

Judge Amy Berman Jackson last week sentenced Mr. Stone to 40 months in prison—a term within the range Mr. Barr had suggested when he overruled prosecutors who recommended a term of seven to nine years. The attorney general’s move generated accusations that he was doing President Trump’s bidding by showing leniency to Mr. Trump’s friend and former political adviser. It even prompted a petition, signed by more than 2,000 former Justice Department employees, demanding Mr. Barr’s resignation.

Before we address these attacks directly, we think it useful to consider a few data points in Mr. Barr’s recent tenure. Notwithstanding his own skepticism about aspects of special counsel Robert Mueller’s investigation, he allowed that probe to run its course. Mr. Barr supported the decision not to prosecute Andrew McCabe, a former deputy director of the Federal Bureau of Investigation and frequent critic of Mr. Trump, despite overwhelming evidence that Mr. McCabe not only lied when he denied leaking information about an investigation but also berated others for the leak to deflect suspicion from himself.

Mr. Barr has said publicly that he believes Mr. Stone’s prosecution was warranted, and that, given his conviction, so is a prison sentence. And the attorney general has pointedly criticized the president—rightly, in our view—for commenting publicly about cases pending in court and before the Justice Department. That is not the behavior of someone doing the president’s bidding.

The criticisms of Mr. Barr’s decision about the Stone sentencing recommendation were unmoored from the case itself. Whatever the line prosecutors thought, the decision to reduce the proposed sentence was reached by others at the department as well, including career attorneys, one of whom signed the lower recommendation.

The Stone prosecution was initiated in an indictment filed by the Mueller prosecution team, for obstructing Congress’s investigation into whether there was a Trump-Russia conspiracy. By the time these charges were brought, it was clear there was no such conspiracy.

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Mr. Stone was also charged with threatening a witness by suggesting that he would kidnap the witness’s dog and by telling the witness to “prepare to die”—but also by vowing that Stone’s lawyers would tear the witness to shreds on cross-examination. There is no doubt about the factual basis for these offenses; Mr. Stone communicated with the witness in text messages introduced into evidence.

The obstruction counts ordinarily would have generated a recommended sentence under the U.S. Sentencing Guidelines of 37 to 46 months or less. A word about the guidelines: They were adopted in 1987, and although at first they were presumptively binding, they are now strictly advisory, owing to a 2005 Supreme Court ruling, U.S. v. Booker.

The recommended sentence under the guidelines shoots up to 90 to 108 months—the range the line prosecutors recommended for Mr. Stone—when threats are involved. But it’s obvious such higher sentences are meant to be imposed only when the threats are real. In this case, the witness was on record as saying he didn’t take them seriously.

The prosecutors’ initial sentencing memo was far from a dispassionate discussion of facts and law. It suggested a link between Mr. Stone and “foreign election interference,” which, quoting Federalist No. 68, it characterized as the “most deadly adversary of republican government,” although the proof never tied Mr. Stone to any such activity. The prosecutors dismissed the witness’s testimony by asserting that a threat doesn’t have to be serious to justify additional years in prison.

Prosecutors are supposed to seek justice, not to play the Sentencing Guidelines as a pinball machine, seeing how many times they can ring the bell, or to use a sentencing recommendation to put public pressure on the judge for a harsh sentence. In a highly publicized and politically fraught case, it was not only proper but advisable for the attorney general to ensure that the government’s sentencing recommendation not serve such unworthy ends.

The much-publicized letter from former Justice Department employees is a curious document. The signers seek to inoculate themselves from criticism as politically motivated by pointing out that many served under Republican attorneys general. Still, it’s hard to escape the impression that the letter writers think of themselves as an elite clerisy, gifted with a superior understanding that should dictate the management of all cases.

The letter writers cite their oath and urge colleagues still at the department to follow it. But it’s lawless to encourage Justice Department lawyers to defy their supervisors, up to and including the attorney general, who take the same oath.

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All that said, the president has severely burdened Mr. Barr’s conduct of his office by repeatedly sounding off about pending cases. He has justified his comments by saying he is the highest law-enforcement officer in the land, and that’s technically true. But it cuts against the president’s narrow interest in at least two ways.

First, he has at least the same obligation as any other actor in the law-enforcement hierarchy to refrain from statements that could prejudice anyone’s chance to get an impartial hearing. Whether he likes it or not, courts will enforce that obligation if he violates it, whether by dismissing charges or by taking other steps to undo any damage.

Second, the attorney general and others at the Justice Department must consider whether public confidence in the department will be shaken if their decisions agree with the president’s expressed views. That would have the perverse effect of encouraging Justice Department decisions with which the president disagrees.

Mr. Barr has agreed to testify before the House Judiciary Committee on March 31. We have no doubt he will do so with the same integrity, and clarity of thought and word he has shown thus far. Frankly, we can’t wait.