By that logic, if I document mistreatment of Northerners and/or Southerners by Lincoln and the Feds, I thereby disprove any moral superiority of the Northern cause?
Our side doesn't need to claim moral perfection. We freed the slaves and broke the power of the aristocracy built on human bondage. I truly believe good men were drawn into service of the CSA, but I also believe that the root cause of the CSA was rotten.
Freeing slaves was good. Thieving, burning homes, bombarding civilians, preventing people from voting, suppressing free speech, thwarting civil law, sectional aggrandizement, violating the Constitution, and forcing states to stay in a union their people didn't want to stay in and weren't required by the Constitution to stay in were bad. That is not to say the South was perfect either. It wasn't.
Iron-plated vessels are not without serious inconveniences, The famous French vessel La Glorie has just laid up in dry dock, when it was found that the contact of the copper lining and the submerged iron plates had established a galvanic current which produced the effect of a voltaic pile, and was completely ruining the armor of the vessel below the water line; the hull was covered by millions of mollusks, among which was a species of shell fish hitherto unknown, and all the wine in the hold was turned into vinegar. [Source: The Daily Picayune, Feb. 20, 1863, of occupied New Orleans]
Or about some of the insanity that happens during war:
Several women ... were arrested yesterday for waving handkerchiefs, etc., at the Confederate prisoners when they went on board the steamer Empire Parish ... [Source: The Daily Picayune, Feb. 22, 1863, of occupied New Orleans]
Might make sense, I guess, depending on what the "etc." was that they were waving. A judge later set the ladies free.