The Confederate States of America only existed for ~4 years.
Slavery existed under the U.S. flag longer than the Confederate flag.
When it comes to issues of the Civil War, though slavery was a tipping point, there were also issues of State's rights and a fear of losing political clout on a federal level that were in play.
Lincoln won the election, the secession started.
The Emancipation Proclamation happened well after the outbreak of the Civil War. Slavery was still federally legal in the U.S. when the first shots were fired.
So to equate slavery as the sole issue in the civil war is to be uninformed and ignorant of the other political issues of the time.
Comparing it to the Swastika is also a false equivalency. The German Government of the WWII era took specific steps to exterminate the Jews. The Confederate Government only had a policy of keeping the status quo. Yes, it was a horrible status quo, but the atrocities committed against slaves were committed by private individuals, plantations and not by official state action.
The idea of allowing that private activity to continue is reprehensible. However, it is very different than having an official state sanctioned policy of extermination.