You know what's interesting, the film John Carter of Mars had a Confederate cavalry officer as the good guy.I'll admit, I don't think it will be plausible enough for you to enjoy! I can see imagine your blood pressure rising. Here's how I see it going. In the first few episodes or even the whole first season, the South will be firmly couched as the "Bad Guys", through and through. Given what you may term as "inaccurate" or "misplaced" stigma regarding the war people are already uncomfortable with experiencing sympathetic Confederate characters.
I wonder if the leaders of the 21st century Confederacy will be Democrats? The leaders of the 19th century Confederacy mostly were. The more Democratic, the more likely the politician was to support secession. Somehow, I'm sure that fact will escape the attention of the writers.BUT, these showrunners won't let that hang around for long. They WILL (at least attempt to) create complex characters on both sides of the story.
You are absolutely right, their show will be an outright failure if it does not immediately dogwhistle to the popular social understanding of the Civil War. But I would not be surprised by any stretch to see them dive into the complicated matter of the original war at some point in the series. But by that point who knows what else will have occurred.