The yeoman farmers who were the backbone of the Confederate army were doing their duty as they saw it. When their states seceded and the Federal army invaded, the paradigm shifted. It was no longer a fight for an economic system and the "peculiar institution". The only options left on the table were resist invasion or meekly submit to it. They fought with courage and honor, not to preserve slavery, but because their home states called them to duty.
I'm certainly not comparing my generation to those who fought in the Civil War, but an analogy of sorts can be drawn between them and those who served in the Vietnam war. Neither I nor anyone I served with gave a rat's a** about South Vietnam or its people. We served because we were called to do so. The vast majority who served did so with incredible courage and dedication. The WAR may have been about protecting a southeast Asian democracy and stemming the tide of Communism, but the FIGHT was about duty, unit honor, military tradition, and the buddy next to you.
That's why I wince whenever I hear someone state that the Civil War was fought to free the slaves. Nonsense. Secession, at least in the deep South, was mostly about slavery, but the war itself was about restoring the Union (if you were a Yankee) and the right of self-determination (if you were a Reb), and the factors I mentioned above for both. I know that's an oversimplification, but that's the basic premise, as I see it.