Correct. This flag is not racism at all.
While it did represent CSA forces, it was created to minimize friendly fire incidents on the battlefield when the Stars and Bars flag was used.
The Southern Cross flag was easier to distinguish in the smoke and haze of battle.
The current rectangular version is essentially a Tennessee design. Most forces used a square version.
All of these flags represented the CSA.
The CSA was defeated and the States reincorporated back into the USA. This also marked the beginning of the end of legal slavery.
The War of Secession was the bloodiest war ever fought, mostly with cannon and rifle fire. In the four years of battle, some 750,000 deaths occurred between 1861 and 1865.
Abraham Lincoln himself was shot and killed by a CSA sympathizers, after the war ended, while attending a comedy play at Ford theater, just days after Lee surrendered to General Grant.
Union troops found these sympathizers and killed them. Booth (the trigger man) was shot, the others were executed by hanging for their crime.
VP Andrew Johnson (who became President after the assassination) and William Seward (Secretary of State).
It could be argued that the last significant casualty of that war was Lincoln himself, and of course, the CSA sympathizers that performed the assassination.
Johnson oversaw the reconstruction and emancipation process.
Congress readmitted the states back into the Union, once they agreed to the terms of the treaty and also participated in the emancipation process.
In December of 1865, the 13th amendment was ratified into law, which ended legal slavery in the United States.