The sectional division that led to the Missouri Compromise (or, more accurately, to the conflicts that made the compromise necessary) was the division between North and South. This division had mostly to do with slavery.
Slavery was, of course, legal in the South and illegal in most parts of the North. By the time of the Louisiana Purchase, there were equal numbers of free and slave states. This meant there was a balance of power in Congress. The purchase upset this balance because the new territories would want to become states and that would mean an end to the equality in the number of free and slave states.
So, the sectional difference that was relevant here was the fact that the North and the South were split on the issue of slavery.