While the flag was never used to justify slavery it was used as a symbol of white supremacy. Even the designer of the flag William T. Thompson said, Our idea is simply to combine the present battle flag with a pure white standard sheet; our southern cross, blue, on a red field, to take the place on the white flag that is occupied by the blue union in the old United States flag or the St. George's cross in the British flag. As a people, we are fighting to maintain the heaven ordained supremacy of the white man over the inferior or colored race; a white flag would thus be emblematic of our cause. ... Such a flag would be a suitable emblem of our young confederacy ... it would soon take rank among the proudest ensigns of the nations, and be hailed by the civilized world as the white man's flag."

After the Civil War it was never flown wide spread until citizens and local governments that opposed desegregation started flying it as a public sign of their resistance. In recent decades plenty of well meaning people have adopted the flag for benign reasons but it has never lost its original message of white supremacy.

As for Bryce Williams there was some racial motivation but the bulk of his suicide manifesto discussed specific (perceived) abuses. He target that reporter because he believed she made a racist comment and he targeted that cameraman because he recorded his outburst when the station fired him. Dylan Roof's manifesto on the other hand was solely race based and he targeted random black people not those he knew personally. Obviously both situations are horrible but the motivations shouldn't be conflated. The LGBT flag stands for acceptance and pride in being openly homosexual. The Northern Virginia Battle Flag was designed to espouse superiority of white men. No straight white people were lynched, discriminated against, raped, enslaved, colonized, ghettoized, or denied opportunities in the name of gay pride.

As for the "desecration of graves" the only one I know of is when the city dug up Nathan Bedford Forrest who was the founder of the KKK and committed war crimes during the war. In that case they moved his body to a private cemetery and was done in a respectful manner. A few random graves were vandalized paint which isn't exactly moral. Although I'm fascinated by the fact that many conservatives are so concerned over this but completely ignore the plight of black people who are oppressed by private and government institutions across the country. No one wants to ban you from purchasing a flag. What should be banned is state and local governments from flying a symbol of white supremacy and of a country that sought to destroy our country.