Slavery was but one of the three points of the trident that served as the catalyst launching the country into Civil War. You had agrarian south, south east, and West beholding to the economic power of the northern bankers / manufacturers, and issue of states sovereign rights versus the centralized government controlled by northeastern special interests. The distinction between southern Democrats and northern Democrats in the 1860's was simply one was willing to make a stand and die for preservation and one that would simply skirt the issue in the name of harmony.
You make an excellent point. Despite revisionism and stupidity, the Republican party of Lincoln was one that promoted industrialists and investors, which as you point out were in the North and had an economic stake in in the wage labor market. The Democrats promoted slavery in conjunction with an agrarian model and the pseudo feudalism that dominated the party.
The Republicans haven't changed very much, they are still the party of industrialists and free marketeers. The democrats remain paternalistic and authoritarian.