Sectional rivalry was part what led to the Civil War, but it was slavery that made the South profoundly different than the North and animated sectional antagonisms. Jefferson's lament was that the South's slaveholders should be pitied due to the menace of slave resistance and rebellion. In the view of Jefferson and many other Southerners, they did not invent slavery but were stuck with it and its evils.
Notably, although the North mostly wanted the slaves freed, they did not want them moving to the North in large numbers when freed. Thus the South was not just stuck with slavery, but in the view of the North, was also after emancipation was to be stuck with the problems of race, poverty, and lack of skills, and with the lack among many slaves of the habits and character needed to make freedom work.
Slavery was a great evil, but it seemed clear to Southerners that emancipation would bring another set of problems that Southerners and Americans were unable to see solutions for. Indeed, in the long view of history, we are still vexed with the problems of emancipation and the legacy of slavery.
My reading of Southern history and of slavery has evolved over the decades. I think that what Americans missed before the Civil War in thinking about slavery and continue to miss on many contemporary issues is that just as the South was stuck with slavery and its evils, we are committed to being a free and self-governing nation. That gives us the glory and the benefits of liberty, but also the problems.
This underpins every issue that Americans deal with. We do best when we recognize that the "blessings of liberty" also come with burdens and problems in American life that require remedies consistent with liberty. To the degree that we fail in that effort, freedom and self-government are also in jeopardy.
“Notably, although the North mostly wanted the slaves freed, they did not want them moving to the North in large numbers when freed.”
Many northern states had enacted Black Codes designed to keep blacks from living there. Lincoln’s own Illinois had them. This site has some fascinating history about slavery in the North:
http://slavenorth.com/exclusion.htm