It's pretty natural, I suppose, being as I am at a college in an unambiguously southern state, that I should be exposed to some fairly strong opinions about the Civil War. Barely any of these, it needs hardly be said, are particularly complementary to the North. I was rather surprised coming down here, actually, to find opinions on the subject still so vehemently held... I mean, the war was nearly 150 years ago, and everyone in the South is now benefiting on equal terms with all the rest of us from the Union of the states. And you just need to look at the history of the 20th century to see how beneficial that union has ended up being to us and to the rest of the world (WWI, WWII, etc).
Be that as it may, my American History class has been quite wonderful in its approach to the era, treating the writings of the period to a rigorous interpretation in light of the country's inheritance from the Founding Fathers. My current understanding of Lincoln's writings leads me to refine my earlier ideas that it is possible to analyze the Civil War from two major perspectives: it was either a war about slavery or a war about states' rights. I do think each of these two aspects was decisive in raising the main issue at stake as an issue divisive enough to split the county, and in the minds of many involved, one or the other was the sole reason for which they were fighting. But there is a more fundamental issue at stake, I think, and it's one that is more intimately connected with the message of the Declaration than either of those two.
I believe that before it was a questions of states' rights explicitly, the dispute at the heart of the war was about how we are to understand rights at all. Perhaps it would be more precise to say that this issue is implied in the states' rights and slavery interpretations. The essential question at the heart of, for example, the Lincoln-Douglass debates, is whether it is accurate to conceive of "liberty" as the capacity to override existing statutory law (here, the Missouri Compromise and the Compromise of 1850) just because a majority wishes to do so. Of course, if you're going to go by the principles laid out in the Federalist papers, to legislate purely according to the will of the majority as opposed to precedent and fundamental law "may justly be pronounced the very definition of tyranny" (Federalist 88).
This becomes a question of greater significance if the fundamental law on which the government is based purports to be a reflection (at least to some degree) of the absolute laws of justice, as we see in the claim of the Declaration to be based on the self-evident truth that "all men are created equal" and that their rights to "life, liberty and the pursuit of happiness" are inalienable. Of course, if the government is such an organic institution, existing in principle from before their actual codification, as Lincoln suggests in his First Inaugural Address (paragraph 13), you really can't throw it off legally (i.e., Constitutionally for Lincoln) unless it itself breaches the fundamental law at its core. The fundamental law moreover is essentially the sum of absolute duties intrinsic to man in virtue of his personhood, not in virtue of majority rule in their favour, while the rights resulting from this fundamental law comprise the freedom to fulfill it. Thus if you reject the government that is trying to uphold the fundamental law, you're rejecting this conception of liberty for excellence in favour of a conception as liberty as the random will of a majority.
Of course, a question that comes up as to whether one could see the South in the Civil War as not intending to reject the fundamental law at the heart of the Constitution at all but to merely change the external form of government that protects it. However, slavery intrinsically violates fundamental law by denying certain people their absolute rights. Looking at the matter chronologically, it is fairly easy to trace the natural progression of thought that would come from support of such an institution. First you have a slave or two, you need to justify the fact that this manifestly contradicts the principles of the Declaration, you naturally enough begin to cry for "states' rights!" "our natural liberties to do what we want with our own property!". Thus you have the concept of states' rights deriving easily from the fact of slavery. Implied in this in the sense that it is necessary to make this view coherent is the redefinition of what it means for Americans to be self-governing.
The idea at the heart of Lincoln's battle for the Union, for the upholding of the American Constitution is that the liberty to which we have a Constitutional right is the freedom to do what is right, not to have equal freedom to do good or evil. If we deny the existence of moral absolutes, civil society disintegrates, Lincoln believes, and it is for this conviction that he came back to politics, debated Stephen Douglass, and finally became president.