Army Brig. Gen. Jeffrey Sinclair, who had been charged with sexually assaulting a female captain who worked for him, walked free Thursday.

Sinclair received a surprisingly light sentence given that he had originally faced life imprisonment and his own defense lawyers seemed resigned to some jail time, asking this week that he not be imprisoned for more than 18 months. Instead, in a decision that surprised many, Sinclair was docked $20,000 in pay and received a letter of reprimand, but was allowed to remain in the military and keep his pension and benefits.

Though there is widespread agreement that the military’s system for dealing with sexual-assault cases is broken and needs to be reformed, the Sinclair sentencing doesn’t fit the standard narrative. The common charge against the military is that it fails to respond aggressively enough to allegations of sexual assault, but this appears to be the rare situation where a case foundered due to a politically influenced, overzealous prosecution.

The Sinclair trial had been a high-profile media event from the start, involving the highest-ranking military officer ever court-martialed in a sexual-assault case. In that climate, and with the Pentagon eager to prove it could be tough on sexual predators on its own, it appears that political pressure influenced the prosecutors going after Sinclair to build a case alleging sexual assault and violent threats that the evidence didn’t support.

Earlier this month, the judge presiding over the case, Col. James L. Pohl, expressed concerns that the prosecutors and commanders had been influenced by political agendas communicated from the Pentagon when they rejected an initial plea offer from Sinclair’s legal team. Pohl said that he was “not convinced beyond a reasonable doubt” of the prosecution’s independence.

As a result of his determination that political influence may have swayed the prosecution, the judge suspended the court-martial proceedings this week and brought the opposing counsels back together to reach a new plea agreement.

The sentence Sinclair ultimately received Thursday was a result of the new plea negotiations, but even in light of the widening cracks in the prosecution’s case it seemed lenient to some observers familiar with military law.

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Pohl has not publicly discussed how he arrived at the sentence he meted out, or why his ruling was less stringent than the punishment that the defense itself had recently asked for. But it is possible that Sinclair would have faced harsher punishment, including being stripped of rank and forced out of the military, if the prosecution had sought an initial plea deal rather than pursuing the more severe charges that eventually fell apart.

Lt. Col. Gary D. Solis, a retired military judge and professor of law at West Point, said “I can’t believe it,” in reaction to the sentence handed down. Sinclair, Solis said, ‘‘is an individual who should not be a general officer. He should have gone to jail and been dismissed from the Army.’’

By trying to secure a conviction that would have supported the military’s case that it doesn’t need outside reform of its legal system, the prosecutors may have allowed Sinclair to get off easy for the crimes the he did admit to—misuse of a government credit card, adultery, and engaging in inappropriate relationships with subordinates. Those crimes, which no one contests, and for which Sinclair is now being punished, might have been enough on their own to get him kicked out of the Army.

For some, even the possibility that undue command influence tainted the prosecution shouldn’t have derailed the trial. “A system shaky enough to be rocked by allegations of undue command influence cannot provide justice for our troops,” said Marine veteran Greg Jacob, policy director of the Service Women’s Action Network. “The Gen. Sinclair case will go down in history as yet another reason we need Sen. [Kirsten] Gillibrand’s Military Justice Improvement Act.”

Rep. Jackie Speier, another advocate of reforming sexual assault prosecution in the military, responded to the verdict with this statement:

“The misuse of government funds should be more than enough to fire General Sinclair. There are plenty of former government employees who have been canned for less. Instead, the judge decided to make him pay back the money he fraudulently charged, pay a small fine compared to his generous taxpayer-funded pension, and let him remain in the military.”

She added: “Even when the world is watching, the military has demonstrated their incompetence at meting out justice. This is another sordid example of how truly broken the military justice system is. This sentence is a mockery of military justice, a slap on the wrist nowhere close to being proportional to Sinclair’s offenses.”

Sen. Gillibrand, whose reform bill proposed using independent military lawyers to prosecute sexual-assault cases instead of commanders, lost that fight in the Senate this month. She released her own statement.

“This case has illustrated a military justice system in dire need of independence from the chain of command,” Gillibrand said.