Slavery was certainly not THE issue, but became AN issue to say the least. Lincoln was not interested in freeing the slaves until it became necessary for him to do so.
But, even if we all agree that slavery was not THE issue, it was still an issue that the south, claimed it had the right to keep. Is this in line with Catholic theology? Is/was it a sin to keep slaves? We can recognize that a lot of modern accounts of slavery (e.g. "Roots") are dramatized, but there was definitely instances of horrible injustices done to Blacks. Were these instances sinful?
From most other issues I believe that the states should have the right to decide. But do states have the right to enslave others? I think "The South Was Right" folks have a hard time defending the enslavement of others.