Slavery, while something that Lincoln did not support, was a heated topic. Secession began largely in part because the South believed that the election of Lincoln was going to jeopardize their ability to own slaves - therefore damaging their economy. Even in the North, there were slavery supporters, and Lincoln essentially had to make the war about preserving the Union - if he made it about slavery, he would lose supporters, which he greatly needed during the course of the war - particularly if he was to gain a second term.

  It must be understood that while Lincoln hated slavery, he still didn't quite regard African Americans as equal; he in fact proposed that if they were to be freed, they should be sent back to Africa, or perhaps given their own piece of land/island in which they could live away from white men. When he finally signed the Emancipation Proclamation, it was less about freeing the slaves, and more about dealing a heavy political blow to the South. It actually did very little at first, but eventually the slaves themselves took it as their official declaration of freedom, and began to run away to the North; many joined the Union army.
  Lincoln wanted to preserve the Union to preserve the image of the United States being indivisible. But he also knew that this was eventually to be a war about slavery (no matter what he claimed initially). He knew that eventually, slavery would prevail throughout the Union, or it would have to be abolished - it couldn't be both.