In Lincoln's own words.
"As President Lincoln wrote in 1862, “My paramount object in this struggle is to save the Union, and is not either to save or to destroy slavery. If I could save the Union without freeing any slave I would do it, and if I could save it by freeing all the slaves I would do it; and if I could save it by freeing some and leaving others alone I would also do that.”"
So, "save the Union" was why he unleashed the dogs of war and started the killings.