People claim its heritage, but the simple fact is that these flags that show or incorporate the Confederate battle flag have only been formally accepted quite recently. Certainly post the civil war anyway. The surprising thing is that, in spite of all the talk of state sovereignty, only two States had their own flag in 1861. The others had to scramble to design flags. Some (like North Carolina) did an excellent job and issued many examples to their troops. Others (like Tennessee) didnt bother. Some (like Florida) produced totally impractical designs that were almost certainly never used; and some (like Georgia) were never able to settle on one design.
In any case, the famous saltire style Confederate battle flag was actually the battle flag of the Army of Northern Virginia. It was rarely used outside of the Eastern Theater of operations during the war.
IOW if the author has a problem with the current mississippi flag, and yet still wants to honor his heritage, I would suggest he uses the State Flag(s) that mississippi DID use during the war (which are very nice designs incidentally). Job done!
Many similar have been preserved from all areas of the war, some with subtle variations (2:1 proportions, hexagonal heraldic stars vs. 5-pointed "mullets" [stars]; Cross of St. George w/ reversed colors vs. Cross of St. Andrew [Gen.Polk was an Anglican bishop], and so on.) and some of completely different design. There was even one cavalry color carried in Texas that was nothing but a Scottish saltire with unit cachets and honors added.