I understand what you mean about thinking with the information we have that has occurred since then, and sorted-out the morality for us presently. But, empathy is still possible. Simply understand that they were caught between a rock and a hard place at a very pivotal time in our history. And, the war itself was an unprecedented experience that changed the nation forever. It still lingers now.
A southerner had this to deal with: "My family, and my church, my community, my neighbor, my friends, and my state are seceding. I feel an allegiance to them before a central government in Washington, DC." Some of the reasons for secession were probably of little importance to most people, just like every other war. You tell them that their home, way of life, and loved ones are threatened, and they rally to the call.
Of course, it's easy to say, NOW, that they were wrong. But, it was not that simple then. I don't personally understand how the Founders created a constitution where people were still property... but, they did. The negro was subhuman. WOMEN were still property!
History has only proven right or wrong, using your measure, by who is winning wars. That's a pretty pathetic use of our higher thinking ability. Who can slaughter one another, wholesale, and manage to hold it together the best, the longest, before one "side" can no longer field an army and keep shooting back. Then, whoever surrenders, is subject to whatever the leaders of the conquerors decide. I can only hope the our better nature, as a species, is operating on a higher level, through the help of a higher power, to keep us intact and finally learn to treat one another in kind. I'm just tired of seeing people resorting to killing each other to prove they are right.