Every symbol has been misused, not just the obvious ones.
The Ku Klux Klan had its own flag (not much seen anymore) but the flag they used was primarily not the Confederate battle flag but the U.S. flag.
In addition, linking the CBF to the Confederate government is tenuous at best. This was not an official flag until late in the war (when it was used as the Naval Jack). In fact, it was rejected as the official flag.
It was the battle standard of various military units as well as the command flag of the Army of Northern Virginia. Those soldiers were fighting for their homeland, not for slavery. See James McPherson's book, Why They Fought. He was or is a professor at Princeton, hardly a bastion of slavery.
So basically what you have left is a small group of segregationist yahoos in the 50s and 60s who hijacked the CBF for their own purposes. That's no reason to ban it - we'd have to ban every symbol (including the Cross - which was flown at Beziers during the massacre of the Albigensians ("kill them all - God will know his own.)")
another shade of ‘miles and miles’ to go
As a "Red-diaper baby" (Communist seed) who hangs with the Communists at Pacifica Radio and other notorious nesting grounds, McPherson is hardly a bastion of anything, except maybe orthodox Marxism-Leninism. He was Clinton's heyboy historian for quick quotes supporting Clinton's social policies and politics, and he and fellow Marxist historian Eric Foner (of Columbia University, the original "little Red schoolhouse") rewrote the guidance and docenting materials for visitors to the national Military Parks like Gettysburg, to inculpate and blacken the Confederate side and their cause, because that was part of Clinton politics, which relied heavily on "booger-man" demonization of the white South and its heroes.
As you say, McPherson is hardly a champion of the old Lost Cause, but even he gets flanked by this new breed of demonizers and segregators, whose battle cry sounds a lot to me like "Crackers to the back of the bus!" And I'm from Indiana, myself.