Well, it prevented the country from dividing into seperate entities.
Also, since Lincoln saw no other option to win the war he freed the slaves to gain allies. I say this because Lincoln said himself that if their was anyway to win the war without freeing the slaves he would do it.
Negative: I believe the CW had the/or close to the highest casualties of any war in history. Over 50,000 men would die in a single large scale battle.
The southern states were left all but completely destroyed. Homes and businesses were destroyed by the Union leaving much reconstruction to be done in areas that were in terrible shape economically. It was decades before many southern states even BEGAN to recover.