Jefferson also wrote the Northwest Ordinance for incorporating the former British territory west of the colonies up to the Mississippi River. In that he specifically forbade slaves. In the census of 1790 and 1800 Virginia was the largest state in terms of population, had the largest delegation in the House of Representatives, and was the economic power until the 1810 census gave New York that honor(?).
The Constitution was a compromise between the small states and the large ones. It required all sorts of compromises. The fear of Great Britain persuading the South, or at least a former colony or two, to rejoin the Empire, was not out of the question. To keep everything together somethings, like moral principles, were lost for on the ground necessary defensive and protective actions.