Or, another question is why did Lincoln NOT free the slaves in 1861 at the onset of his war?
That's very simple: (a) he didn't believe that he had the Constitutional authority to free all slaves; (b) he didn't have control of the slaveholders in the rebellious states; and (c) he believed that the rebellion had to be successfully put down before abolition was feasible. Nevertheless, he instituted or agreed to numerous interim anti-slavery measures long before issuing the Emanicipation Proclamation. (See Abraham Lincoln's Evolving Stance On Slavery From 1861-1863)
Lincoln very skillfully walked a fine line as a pragmatic abolitionist between the radical Republicans on one side and the conservative Northerners on the other, and I don't see how anyone can seriously question his effectiveness in ending slavery in the final analysis.