Whether Thomas Jefferson's vision of the future of America was coherent was unclear then and remains unclear now.
Jefferson, like most of his founding-father contemporaries, was steeped in one version of classical history: Roman history as a morality play. Jefferson and many, many of his revolutionary peers assumed that yeoman farmers--Cincinnati--were the only possible social class that could maintain a free republic. They all believed that Rome was a great, free Republic because of its fiercely-independent farmers who nevertheless loved their city and would--like Cincinnatus--drop their ploughs and instantly take up their swords to defend (and conquer), and then return to their ploughs after the war was over.
The history that he and his peers had been taught was that the two centuries around the start of the Christian era saw the transformation of Rome from a virtuous farmer's republic into an unequal, commercial, corrupt, imperial city of plutocrats and proletarians. The wealth of conquest corrupted the Republic, so their teachers taught them, transforming Italy into a land of plutocrats, moneylenders, slaves, and driving the former self-sufficient yeomen off their land into the city. There they subsisted on bread and circuses and became proletarians--the Roman mob which was such easy prey to demagogues. Thus the virtuous city of Rome degenerated into the unequal, commercial, corrupt, imperial city of proletarians and plutocrats over which demagogues and then demagogues fought.
The Emperor Augustus stabilized the situation at the price of the Romans' liberty, but only for a while. Afterwards the best that could be hoped for was the benevolent rule of a wise autocratic emperor. And after a run of five--Nerva, Trajan, Hadrian, Antonius Pius, and Marcus Aurelius--Rome's luck ran out.
Jefferson and his followers saw the transformation of London into an unequal, commercial, corrupt, imperial city as a similar threat to British liberty. Indeed, what they saw as the threat of the spread of imperial corruption from London across the Atlantic was one of the reasons that they made the American Revolution.
Republican virtue was to be found only in the countryside, where people worked hard and wrested their living from the soil. But Jefferson did not set his hand to the plough. And his family’s plantations were arenas of vice and domination to a degree that far surpass the corrupt London of George III Hanover. Jefferson did, however, free those of his slaves who were descended from himself.
Making this historical morality play very real indeed to Jefferson's generation was their firm belief that eighteenth-century Britain was repeating Roman history. Eighteenth-century Londoners saw their civilization as in an "Augustan Age"--and the rebel American colonists saw that as no good thing. That is why they rebelled. Rebel colonial grievances up to 1775 were not because the tyranny of London was then so burdensome--stamp taxes, tea imports, arbitrary royal governors, continental-system trade restrictions, and even the closing of Boston's port were not intolerable, but the precedent that Americans were not citizens but subjects was intolerable in the context of what they saw as Britain's steps along the road of imperial destiny. And after the Revolution was won, one of Jefferson's highest priorities was to keep the cycle of urban-imperial corruption and subsequent loss of liberty from happening again by making sure that Philadelphia and New York did not become Rome. In the eyes of Jefferson and company, Republican virtue was to be found only in the countryside, where people worked hard and wrested their living from the soil.
And while imperial Britain’s rule was a bad thing in Jefferson's view, the agrarian economy that imperial Britain’s mercantilist policies had gardened its North American colonies into was a good thing because it kept Americans close to the soil, and hence virtuous.
The Jeffersonian current in American politics was indeed strong. A generation after Jefferson, the president was Andrew Jackson. Andrew Jackson's enemies were: Amerindians, bankers, corrupt government contractors, and anyone who favored literacy or property tests that kept the vote from the (white, male) rural adults with their hunting rifles whom Jackson as president believed had come down the Mississippi at the end of 1814 and so enabled him to win the Battle of New Orleans. A Jefferson-Jackson United States would have been rural, Anglo-Saxon, Southern and Border-Southern, and not a technological-leader but rather a technological-follower nation.
What would have been the long-term consequences if America had not taken the Hamiltonian turn? What would the world in 1900 have looked like if the United States had focused on specializing in its comparative advantage of resource-intensive products and bought most of its manufactures from Britain and Europe?