Nearly every reputable historian agrees that Lincoln freed the slaves as a war measure. It was a brilliant tactical move. Having been badly battered during the first 2 years of the war, and fearing British and/or French intervention on the side of the Confederacy, he issued the Emancipation Proclamation, which just about guaranteed that the Europeans would not intervene. The Emancipation Proclamation and the loss of Jackson were the twin blows in the first 6 months of 1863 from which the Confederacy never recovered.
The Confederate political leadership, overruling the recommendations of its generals (including Lee and Patrick Cleburne in the West, among others), would not support a plan to emancipate the slaves who fought for the South. They only adopted such a plan in 1865 when it was too late. Tragically, from the southern perspective, Cleburne was denied further promotions as punishment for advancing this plan in 1862, in spite of his sterling battlefield record.
One correction. Even then the southern congress could not bring itself to freeing the slaves. If you read the legislation, here , which was submitted for debate in February 1865 it calls for the enlistment of 200,000 black troops and promises nothing in return.