I hope you'll excuse me reposting something I wrote some time back, as while it is aimed much more broadly than your question here, it does cover the Emancipation Proclamation within it (if that is all you want, skip about half-way down).
-Abe Lincoln's First Inaugural Address, March 4, 1861
It is a canard of Confederate apologia that war aims must be perfectly opposite. It is simply a fact that in his public statements, President Lincoln made clear that he was not out to abolish slavery, and that the Union undertook its campaign to prevent southern secession, since, in his words, the Union was perpetual, that "Perpetuity is implied, if not expressed, in the fundamental law of all national governments". So, their logic goes however, that if the Union did not launch its war to end slavery, then slavery was not the cause of the war. Nothing could be further from the truth. This work will attack this position from multiple angles, demonstrating not only that the protection of slavery was a principal aim of southern secession, but that the mere right to secede was never a clearly established legal one, at best subject to major debate, and indeed, only entering the national discussion as slavery became a more and more divisive issue for the young nation, and further, that aside from legal/Constitutional concerns, secession as performed by the South was an immoral and illiberal act.
Descending from these general principles, we find the proposition that in legal contemplation the Union is perpetual confirmed by the history of the Union itself. The Union is much older than the Constitution. It was formed, in fact, by the Articles of Association in 1774. It was matured and continued by the Declaration of Independence in 1776. It was further matured, and the faith of all the then thirteen States expressly plighted and engaged that it should be perpetual, by the Articles of Confederation in 1778. And finally, in 1787, one of the declared objects for ordaining and establishing the Constitution was "to form a more perfect Union."
-Abe Lincoln, March 4, 1861
The idea, often pithily expressed by the factoid of "The United States are vs. The United States is", that as originally envisioned the several states were essentially independent nations held together by a weak Federal entity for the common defense, and that it was the Civil War which changed this relationship, is an utterly false one. While Lincoln is perhaps a biased figure to appeal to, his observation nevertheless points to the sentiments of the Articles of Confederation, and the Constitution that followed, which speak of perpetuity and union at the time of founding.
At the time of drafting, James Madison, the "father" of the Constitution, noted in a letter to Alexander Hamilton that "the Constitution requires an adoption in toto, and for ever", because "compacts must be reciprocal". Likewise, while reading out the letter to the New York Ratification Convention, Hamilton expressed similar sentiment in response, that "a reservation of a right to withdraw […] was inconsistent with the Constitution, and was no ratification." Similarly, Washington, serving as President of the Constitutional Convention, noted "In all our deliberations on this subject [the perpetuity of the government] we kept constantly in our view that which appears to us the greatest interest of every true American, the consolidation of our Union, in which is involved our prosperity, felicity, safety, perhaps our national existence".^1 While it is certainly true that the Constitution made no explicit mention either way as to the correctness of secession, and that some expressed trepidation at the thought secession could not be an option, it is equally true that the issue was addressed at the time of ratification, and it was anti-secession Federalists such as Hamilton and Madison, with clarity of their position, who shepherded it through.^2
But if secession was not a clearly reserved right from the beginning, when did it begin to enter the "conversation"? Well, the fact of the matter is that the importance of the aforementioned perspective is itself a product of the post-war revisionist works. It is misleading at best to speak of state loyalties above country and in fact, it is demonstrable that it was the supremacy of national loyalties that helped to delay the divisiveness of slavery that started to nose itself into the national conscious with the 1819 Missouri Crisis^3a. Rather than being an inherent weakness of the Federal government as created by the Constitution, the apparent weakness of the Federal government was a creation of southern politicians specifically working to protect their slavery based interests from the mid-to-late 1820s on-wards, forcing compromises that maintained a balance between slave and free states. To quote Donald Ratcliffe:
The strengthening of national power in the 1860s reflected, in part, the restoration of the political situation that had existed before the South began to impose its deadening hand on the Union in the thirty years before the war.^3a
Now, while demonstrating that the doctrine of states' rights was not a constant over the first 80 years of United States politics, it still stands to show that, far from being a "flavor of the month", as some 'lesser' apologists assert, slavery was an absolute central component of Confederate war aims, and the defense of their 'peculiar institution' surpassed any principled defense of States' Rights. The simple fact of the matter is, that far from simply asserting their moral right to own another human being for the use of their labor, the southern states' need for slaves was intimately tied to their political and economic fortunes, to the point that any claim of political or economic reasons for secession can not be separated from the root base of slavery.
When Lincoln was elected in the fall of 1860, the South was terrified. Whatever his prior declarations that whether he wished to or not, he had no power to interfere with the institution where it existed, Lincoln was nevertheless a Republican, a political party founded on its opposition to slavery, and at its most mild, committed to stemming the further spread as statehood spread westward. While committed, absolute abolitionism was a vocal minority on the national stage, the simple limiting of expansion presented a long term existential crisis to the slaveholding states. Every free state to enter the Union represented additional Senators and Representatives to immediately exercise power in Congress, and represented the growth of power not only in future Presidential elections, where anti-slavery parties could continue to gain momentum, but in the long term even foreshadowed, one day, a strong enough majority to abolish the institution once and for all through Constitutional Amendment. And it wasn't only that Lincoln and the speedy rise of the Republican party threatened a political threat to slavery, but also that, due to the 3/5 Compromise, the existence of enslaved populations represented a significant boost to the electoral power of the slave states.^3b
Economically, the fortunes and viability of the South were intertwined with slavery so closely as to be inseparable. Turning to the Nullification Crisis of the 1830s, Calhoun observed that slavery was the undercurrent of economic disagreements with the northern states, although he was by no means the first or last:
I consider the tariff act as the occasion, rather than the real cause of the present unhappy state of things. The truth can no longer be disguised, that the peculiar domestic institution of the Southern States and the consequent direction which that and her soil have given to her industry, has placed them in regard to taxation and appropriations in opposite relation to the majority of the Union, against the danger of which, if there be no protective power in the reserved rights of the states they must in the end be forced to rebel, or, submit to have their paramount interests sacrificed, their domestic institutions subordinated by Colonization and other schemes, and themselves and children reduced to wretchedness.
While fears over the continued viability slavery had been a driving concern for southern politicians for at least a decade by then, it was the Nullification Crisis that clearly established the unbreakable ties of slavery and economic concerns. To quote Richard Latner:
South Carolina's protest against the tariffs of 1828 and 1832 was only a surface manifestation of profound planter fears, real and imaginary, that a hostile northern majority would subvert their slave system. The crisis laid bare southern anxieties about maintaining slavery and evidenced a determination to devise barriers against encroachments on southern rights.^4