It is impossible to know for sure if the Civil War would have come out any differently had Lincoln not infringed on civil liberties. The most likely way in which things could have been different would have been in Maryland. Maryland was one of the "border states" that had slaves but which stayed in the Union. At least part of its decision to stay in the Union can be credited to Lincoln's suppression of Southern sympathizers in that state. If Maryland had gone with the Confederacy, things might have been very different strategically, with Washington DC cut off from the North and with the South bordering New Jersey. Without the buffer of Maryland, the North might have been more vulnerable to Southern invasions.