Had it not been for the issue of slavery the Federals would've had very little moral ground on which to stand in prohibiting secession. Because of this peculiar institution and preservation of it was the actual reason that secession was sought, meant that those seeking to save the Union were left with the moral higher ground.Remember that the war started when the rebels attacked federal property.
The Confederates seceded in an effort to preserve a way of life which was rapidly becoming antiquated and was eventually doomed. Slavery was a very visible and extremely objectionable symbol of that way of life, and was indeed an integral part, as was the legislated inferiority of free blacks.
Indeed, in their desire to hang on to the ways of the past they resembled environmentalist Luddites more than modern conservatives. Ironically, to even stay in the war as long as they did they had to become what they opposed, an industrialized state with increasing federal perogatives, particularly regarding the military.
-Eric