There was no reason the South shouldn't have been able to withdraw from the union under the basic tenets that formed the foundation of the country. The Declaration of Independence clearly states that governments are formed by men, and when men no longer feel that their government is serving their needs they are free to leave and start a new one.

To say that they didn't mean that to apply to the United States as well is to completely lack understanding of the frame of mind of the founders.

Unfortunately, slavery is such a morally repugnant institution that we have allowed the issue to be clouded by the fact that the North ended it. Saying that the North was the right side in the Civil War is basically an ends justify the means argument and wouldn't be any different then saying it's okay to deny due process to a particularly offensive criminal.