I did some reading about what Jefferson may have thought about the Second Amendment.
Here are some quotes:
"No freeman shall be debarred the use of arms (within his own lands or tenements)." --Thomas Jefferson: Draft Virginia Constitution (with his note added), 1776. Papers 1:353
"It is more a subject of joy [than of regret] that we have so few of the desperate characters which compose modern regular armies. But it proves more forcibly the necessity of obliging every citizen to be a soldier; this was the case with the Greeks and Romans and must be that of every free State. Where there is no oppression there can be no pauper hirelings." --Thomas Jefferson to James Monroe, 1813.
"Uncertain as we must ever be of the particular point in our circumference where an enemy may choose to invade us, the only force which can be ready at every point and competent to oppose them, is the body of neighboring citizens as formed into a militia. On these, collected from the parts most convenient, in numbers proportioned to the invading foe, it is best to rely, not only to meet the first attack, but if it threatens to be permanent, to maintain the defence until regulars may be engaged to relieve them."
--Thomas Jefferson: 1st Annual Message, 1801. ME 3:334
"I think the truth must now be obvious that our people are too happy at home to enter into regular service, and that we cannot be defended but by making every citizen a soldier, as the Greeks and Romans who had no standing armies; and that in doing this all must be marshaled, classed by their ages, and every service ascribed to its competent class."
--Thomas Jefferson to John Wayles Eppes, 1814.
"The constitutions of most of our States assert that all power is inherent in the people; that... it is their right and duty to be at all times armed."
--Thomas Jefferson to John Cartwright, 1824.
And here is the best:
"Laws that forbid the carrying of arms . . . disarm only those who are neither inclined nor determined to commit crimes . . . Such laws make things worse for the assaulted and better for the assailants; they serve rather to encourage than to prevent homicides, for an unarmed man may be attacked with greater confidence than an armed man."
--Thomas Jefferson, quoting Cesare Beccaria in On Crimes and Punishment (1764).
Jefferson clearly envisioned an armed populace to protect the nation, but not solely to protect the nation. He envisioned an armed populace so that it could protect itself from criminals. One of these purposes is somewhat anachronistic - the other is not.