Lincoln was tired of the fighting. After being witness to the bloodshed of the war, why would he want to be harsh on the south? They had already lost the majority of their work force. Before y'all jump down my throat for being racist, I mean all of the poor men who worked their own farms and had joined the Confederate army to earn money for their families and a chance at a better life, not the recently freed slave population. Almost an entire generation of southerners had just been wiped out. Lincoln knew that the only way to hope for healing between the north and south was to allow the south the ability to recover. Unfortunately, a Marylander with southern sympathies decided it would be a brilliant idea to shoot Lincoln shortly after the end of the war. The men who followed Lincoln were far less lenient with the south than he would have been, which is what basically led to years of resentment, hatred, and, ultimately, Jeff Foxworthy.
Morpheus...freeing the slaves was never a goal of the war. The Emancipation Proclamation was a ploy by Lincoln to keep England from joining the war on the side of the Confederate States of America.