The South seceeded over sovereignty issues (of which slavery had a minor role, but economics had more), and the North fought to preserve the union in order not to lose though states which grew the resources that kept their industrialized economy afloat. The North didn't have a problem trying to recruit slave-owning generals like Robert E. Lee, nor was slavery illegal in the North.

I've always thought of Lincoln's later comments on slavery as the kind of "spin" that politicians always put on wars to sell them to the populace. Well, it worked -- we still act like the Civil War was fought by a valiant free north to help the oppressed blacks. Not even slightly true, although the war did have the positive outcome of ending slavery.