It is obviously not my call, but Mississippi probably should remove the confederate battle flag and replace it with a Magnolia blossom, which I believe is the state's official flower.
Or, they could replace the battle flag with a single star on a blue background, but then again, someone would eventually suggest that they're replacing one confederate symbol with another - the "bonnie blue" - so never mind.
I'm reluctant to erase history to the evil but popular modern-day cause of Presentism, but some symbols, often egregiously used for post-Civil War experiences (KKK lynchings and the like), are clearly painful reminders to many Americans. I think most people respect that, and should.
Like the Holocaust, we should never allow history to be erased so we forget the pain and violence experienced (or, even caused) by our forebearers, which serve as an important reminder - never again. Every nation, every people, have painful historical episodes. It is helpful to be reminded of them so they are not repeated.
And while Mississippi is at it, they should consider replacing one of their two statues in the US Capitol, one Jefferson Davis (don't destroy it, but place it in a museum somewhere, since he also served the US in other ways, including as US Secretary of War during the Franklin Pierce Administration). The state's other statue is James Z. George, who after the Civil War became an influential US Senator who helped shape the Sherman Anti-Trust Act.
Senator George was not alone among former confederates who did much to help reunite our country after the "Great Unpleasantness." The confederacy's first commanding general, Joseph E. Johnston (not believed to be a relative), served a term in Congress from Virginia and was a pallbearer at Gen. William Tecumseh Sherman's funeral (he caught pneumonia from the experience and died a few weeks later).
Why is that important? Johnston commanded the confederate army that opposed Sherman's "March to the Sea," (see: Gone With the Wind) and many of his novel defensive tactics are reportedly still taught at the US Army's War College today. Johnston, who surrendered his army about two weeks after Lee surrendered at Appomatox, did much to help reunify the nation. As did Lee.
The great state of Mississippi has many other great historical icons they should honor. I'll leave it up to them to decide, as the law and respect for the people of the state require.