Latest developments suggest that the President's destruction of the invisible wall between the White House and the department and the obliging behavior of Barr may already mean that the question of possible political interference will haunt almost every large-scale Washington case for the rest of the current administration.
That's perhaps not surprising since the furor follows a string of moves by the attorney general that have appeared designed to shield the President and have pulled the Department into the political fray, notwithstanding Barr's warning last week that Trump's tweets make it impossible for him to do his job.
The prosecutor statement and recent developments reflect how Trump's relentless pressure on the Justice Department has at the very least left the impression of politicization -- almost as damaging to confidence in the law's independence as actual interference.
Such an outcome is why many previous Presidents have sought to avoid the impression of interfering in the Justice Department. Trump by contrast has often given the impression that the law enforcement instruments of the US government should be pressed into service to help him.
Barr is under fire not just for the Stone case, but for fulfilling Trump's demands to probe the roots of the Russia investigation and for accepting so-called evidence on Joe Biden from the President's personal attorney Rudy Giuliani from the caper in Ukraine that triggered Trump's impeachment.
The White House is meanwhile taking new efforts to discredit the Mueller investigation, and to tarnish the department's top career leaders as partisans who sought to thwart his election.
Trump, along with his political media complex, is making a case that the problem is that the traditions and personnel of the department itself are rotten rather than the political pressure he and his acolytes are heaping upon the entire department.
"What we have been seeing again and again is that the Department of Justice has been politicized and the Attorney General Barr is trying to correct it, " Vice President Mike Pence's chief of staff Marc Short said on CNN's "State of the Union" Sunday.
New moves in the Stone case
The latest trigger for the Justice Department crisis -- the Stone case -- will be in the spotlight Tuesday when a federal judge holds a scheduling call in a case involving the President's friend that is riddled with claims of political interference.
The magnitude of the worst credibility crisis at the Justice Department in decades is revealed by a statement drawn up by Republican and Democratic former department officials that has now attracted more than 2,000 supporters.
"Mr. Barr's actions in doing the President's personal bidding unfortunately speak louder than his words," the letter said.
The officials called on Barr to resign, but since they had no confidence he would do so asked career officials "to take appropriate action to uphold their oaths of office and defend nonpartisan, apolitical justice."
Gene Rossi, one of the prosecutors who signed the document explained his reasoning to CNN's Brooke Baldwin.
"Bill Barr has decimated the esprit de corps and the rule of law in the Department of Justice," Rossi said.
Rossi expressed concern about the Stone case, Barr's comments on FBI and CIA "spying" against Trump in the 2016 campaign, his misrepresenting of the Mueller report's recommendations and his decision to reexamine the case against former national security adviser Michael Flynn as signs of troubling politicization.
He warned Barr was destroying the "fabric" of the Justice Department -- the undertaking to "to look at a case fairly and impartially and regardless of whether you are an 'R' or a 'D' or an independent -- if you have broken the law. No one is above the law including the president of the United States."
One former prosecutor, Joseph Moreno, however, explained that while he respected the signatories to the letter, he was not as far along as they were in his concerns over Barr, pointing out that Robert Mueller was allowed to complete his investigation.
"The attorney general has an extremely difficult position. And I think that statements he made like the one last week to ABC news where he said, 'Look, the tweets have to stop. You're making it impossible to do my job,' that's important," Moreno told CNN. "So I think while this change to the (Stone) sentencing recommendation to many people may seem like wait a minute, that's a bridge too far. I think in the big scheme of things, this issue is being blown out of proportion."
Philadelphia US District Judge Cynthia Rufe, who heads the independent Federal Judges Association, told the paper the group "could not wait" until its spring conference to discuss the crisis.
Trump backs Barr
Given Trump's sensitivity to outside criticism, especially from subordinates, some observers questioned whether Barr was treading on dangerous ground in his interview -- even though he has made repeated efforts to protect the President.
But a White House official told CNN's Jim Acosta on Monday that the President still had confidence in his attorney general, amid the increasing calls for him to resign.
The White House, as it often does, has used the controversy over Stone to stage a counter-offensive, as the President seeks to discredit all allegations against him in election year.
Short told CNN's Dana Bash on "State of the Union" Sunday that the President felt that the justice system was biased against him.
"The President's frustration is one that a lot of the Americans have which feels like the scales of justice are not balanced anymore," Short said. "And when someone like Roger Stone gets a prosecution that suggests a nine-year jail sentence which is four years above the sentencing guidelines ... they feel it is unusual."
Some observers did consider the Stone recommendation harsh. But Trump's tweet and the subsequent move by the Justice Department to overrule its own prosecutors left a clear impression of a conflict of interest and political interference in the case.
So did the department's revised filing -- which read more like a defense lawyer's submission than a prosecutorial document -- a factor that could play into Judge Amy Berman Jackson's deliberations on the appropriate sentence for Stone.
The President last week slammed the Stone case as "a miscarriage of justice" and added in a tweet: "This is a horrible and very unfair situation. The real crimes were on the other side, as nothing happens to them."
Yet Stone was convicted after a trial by a jury -- and was accused of attacking the rule of law on seven charges, including obstructing the investigation into whether the Trump campaign conspired with Russia to meddle in the 2016 election.
While the sentencing issues has allowed the President to fog the details of the case, the argument that Stone did not receive justice appears to be on thin ground.
In the past two weeks, the Justice Department has twice ordered US attorney's offices around the country to participate in what some of them perceive as politically charged actions, according to people familiar with the matter, including on Barr's effort to crack down on "sanctuary cities."