First of al, as you well know, the Emancipation Proclamation did not, in fact, free a single slave. Lincoln intended it that way.
Second, he is famously quoted as saying that if he could hold the Union together without freeing a single slave, by freeing some slaves, or by freeing all the slaves he would have done so. In fact, in his first inaugural address (before the Civil War began) Lincoln said he would not interfere with slavery in states where it existed.
For many who fought for the South, the war was about protecting their home from an invading army. Many Southerners were infuriated with high tariffs that benefited Northern businesses but placed a burden on Southerners who bought foreign goods. These tariffs also were used to fund federal projects primarily in the North.
In addition, black Southerners served in the Civil War as well, on the side of the South. Were these people fighting to defend an institution that amounted to genocide of their race? Or were there other reasons for this phenomenon?
Lincoln ran roughshod over the Consitution, started the first illegal income tax, and basically destroyed the founding concepts of this Union of States. He had a Congressman arrested for criticizing him.
Slavery was on the way out and had Lincoln and the Republicans left the institution alone it would have died a natural, peaceful death. While many in the South, notably Davis, wanted to educate tehm, Lincoln and the Radicals set them free with no education so they could use them (uneducated, ignorant people being much easier to manipulate) -- the exact same racist trick that the liberal Democrats use today, and in both cases, I believe they knew exactly what they were doing.
As for secession itself, the South was kept in the union by force. Jefferson Davis said, “A question settled by violence, or in disregard of law, must remain unsettled forever.” America is a constitutional republic. Our government is based not on the rule of a king, a president, a parliament or a legislature, but is based on a document created over 200 years ago. Our government is based on the rule of law, and a war cannot, and should not, “settle” a question of legality.