Kelly's comments, made during an interview with Fox News' Laura Ingraham, re-ignited a political firestorm sparked earlier this year about whether Confederate generals should still be venerated with statues in American cities.
Specifically, he was asked about a decision by a Virginia church to remove plaques celebrating Lee and George Washington.
"I would tell you that Robert E. Lee was an honorable man," Kelly said. "He was a man that gave up his country to fight for his state, which 150 years ago was more important than country. It was always loyalty to state first back in those days. Now it's different today. But the lack of an ability to compromise led to the Civil War, and men and women of good faith on both sides made their stand where their conscience had made them stand."
In defending Kelly's comments to reporters on Tuesday, Sanders accused reporters of creating a false narrative around them.
"Because you don't like history doesn't mean that you can erase it and pretend that it didn't happen," Sanders said. "I think that's the point that Gen. Kelly was trying to make. To try to create something and push a narrative that simply doesn't exist is just frankly outrageous and absurd."
Sanders also referenced the historian Shelby Foote, who in the 1990 Ken Burns documentary "The Civil War" made a similar argument that a failure to compromise was at the root of the problem.
"It was because we failed to do the thing we really have a genius for, which is compromise," Foote said. "Americans like to think of themselves as uncompromising. Our true genius is for compromise. Our whole government's founded on it. And, it failed."
Noting that she didn't want to re-litigate the Civil War, Sanders mentioned Foote's comments and said there were "a lot of historians that think that and there are a lot of different versions of those compromises."
Burns himself responded to that argument Tuesday in a tweet, saying: "Many factors contributed to the Civil War. One caused it: slavery."
A number of historians and journalists were sharply critical of Kelly's comments and Sanders' defense, accusing the chief of staff of misunderstanding the key issue over which the Civil War began.
"I think Kelly's comments marginalize the central issue of the war, which was the expansion of slavery," Edna Greene Medford, a professor of history at Howard University, told CNN. "Absolutely, there were differences over the expansion of that institution which led to secession and secession led to war, but to conclude that it's about people not being able to compromise, it's just too simplistic."
Jim Grossman, the executive director of the American Historical Association, called the idea of compromise an "interesting" notion, and asked what compromise there could possibly be.
"George W. Bush has referred to slavery as 'America's original sin,'" Grossman said. "What compromise was available once states had made it clear that they would secede from any nation that would interfere with their right to own human beings? Prolonging the enslavement of those people?"
What's more, Grossman added, the declarations of secession made clear that states were "seceding from the union to preserve the institution of slavery."
"That would suggest to me that anyone who thinks there could have been a compromise is either engaging in the fantasies of the old South that were created at the end of the 19th century, or feels that the enslavement of people could have been prolonged in order to maintain peace."
The debate over Civil War history is long-simmering but has reached new heights during the Trump administration. That heightening and Kelly's comments come at a time during which President Donald Trump has been scrutinized for his response to racial acrimony.
Some critics drew parallels between Kelly's comments to Ingraham and Trump's inciting remarks earlier this year in which he blamed both sides for the deadly violence in Charlottesville, Virginia, that left one counter protester dead after a car crashed into a crowd.
Many attempts at compromise
Others, like Judith Giesberg, a Civil War historian at Villanova University, pointed out that the United States offered a number of compromises before the war erupted in 1861. She and others pointed to the Corwin Amendment, a proposed constitutional amendment that would have prohibited Congress from abolishing slavery.
"That was the ultimate attempt to compromise," Giesberg said of what would have been the 13th Amendment. "It actually passed Congress which is quite stunning if you think about where the country was in 1865 passing a 13th Amendment that prohibited slavery."
When he ran for president in 1860, Abraham Lincoln said repeatedly that he wanted to prevent the expansion of slavery into the western territories that had not yet become states. But he said he would not seek to interfere with slavery where it already existed.
The author and journalist Ta-Nehisi Coates, who has written extensively about the Civil War, wrote on Twitter that the "notion that Civil War resulted from a lack of compromise is belied by all the compromises made on enslavement from America's founding," noting the existence of the Three-Fifths Compromise, The Missouri Compromise and the Kansas-Nebraska Act among others.
"Shocking that someone charged with defending their country, in some profound way, does not comprehend the country they claim to defend," Coates tweeted.
In the same interview with Ingraham, Kelly made an argument about applying the standards of right and wrong today to events that happened centuries ago.
"I think we make a mistake, though, and as a society and certainly as, as individuals, when we take what is today accepted as right and wrong and go back 100, 200, 300 years or more and say what those, you know, what Christopher Columbus did was wrong," he said. "You know, 500 years later, it's inconceivable to me that you would take what we think now and apply it back then."
When it comes to Lee and the Civil War though, historians rejected the notion that modern-day values were being projected onto past events.
"I think it would be preposterous to criticize a pope in 900 AD for not having contemporary ideas about ethnic diversity. But when we are talking about the American Civil War, there were contemporaries of Lee who made a very different decision than he did," Fitzhugh Brundage, a history professor at the University of North Carolina at Chapel Hill, said, noting that there were "plenty of Americans who believed that slavery were such an evil that they were willing to put their lives on the line to destroy [it]."
"That's not somehow me being present-ist and imposing my values on them. Frederick Douglass, Abraham Lincoln and others had a different set of values," Brundage said. "So I think we could judge Robert E. Lee against his own contemporaries without having to impose our own present-day moral values."