Stop quoting out of context. A fuller version of the quote is:
I am a little uneasy about the abolishment of slavery in this District, not but I would be glad to see it abolished, but as to the time and manner of doing it. If some one or more of the border-states would move fast, I should greatly prefer it; but if this can not be in a reasonable time, I would like the bill to have the three main features---gradual---compensation---and vote of the people---
In other words, Lincoln was all for emancipation in the District of Columbia. Lincoln had propose abolition in the District years before when he was a Congressman. But he had some scruples about how emancipation was going to be implemented by the 1862 legislation.
I still don't enjoy this. These misquotes are a big reason why.
Lincoln was quite clear that he was no abolitionist and that the North did not go to war over slavery. The Northern dominated US Congress passed a resolution in 1861 saying exactly that.