Hmmm. Could work. I'd stick with that, but maybe reverse which one is Pro and Anti-Slavery. Think of it: A rural Plantation based economy doesn't have the tools to maintain Ironmen. Factories do. You could have the war be between a rural, more magically based North versus a more urbanized/mechanized South who shackles Ironmen to their factories.
Just a thought to switch things up. It also would make the winners more sympathetic (not that the original Union wasn't) by transforming them from an Unstoppable Industrial Juggernaut into a Rag-tag bunch of Misfits trying to right a great wrong against terrible odds. RL Americans love underdogs. It also lets you use the Magic v Tech theme in the form of a direct contest. That said, this world's war doesn't need to end so clear-cut and clean. Perhaps there's a short era of splintering during and after the war before re-unification can take place. Maybe only the Slavery issue is resolved while both Nature and Tech take a hit.
But above all else, if you plan to flesh out Pseudo-America's Civil War (seriously, we need a name for this Empire), it has to be big. Not just in casualties or in numbers, but in ideas. The American Civil War was our culture's Odyssey. A fictional version of it should carry no less grandiosity.
RL New Orleans was allied with the South, but got itself swiftly occupied by the Union in short order. Personally? I'd make Coterois into this world's Casablanca, a place that, during the war, acted with great autonomy due to its remoteness, acting as both City of Spies and gateway out of a war-torn nation. During the war, Coterois was of great strategic importance (it was hard to chase smugglers into the swamps and its sailors were experienced enough to run blockades with ease), that it was the unoffical middle ground, where agents of the North and South could meet, both for diplomatic purposes, espionage and occasionally assassination. After the war, the city became a safe haven for deserters and veterans alike, particularly the more violent element who couldn't let go of the carnage they saw.
Nothing so far beyond that Poe idea. I'll think on it.