All and all, the article above is a delightful, if deceptively "mainstream" (and thus more likely to be inaccurate) version of history/constitutional law. That said, both it and the subsequent discussion it has produced are fraught with historical error. I would accordingly point out that the "point" where the federal government came out on top, at least in the estimable eyes of that founder-of-founders Thomas Jefferson, happened well before either the Civil War or the Income Tax. It happened instead sometime in 1826 shortly after Jefferson died, and several of his final letters plainly state as much. Consider:
A few months before his death Jefferson began preparing a counteroffensive against a legislative program of John Quincy Adams to federalize the system of road, canal, and harbor improvements under an expansive reading of the power to "regulate commerce." In December 1825 he actually drafted a bill to be proposed by one of his surrogates in the Virginia legislature that is strikingly similar to the so-called "nullification" bills on gun rights and the sort that are finding favor in state legislatures today. It proclaimed in part:
And as a further pledge of the sincere and cordial attachment of this commonwealth to the union of the whole, so far as has been consented to by the compact called "The Constitution of the United States of America," (constructed according to the plain and ordinary meaning of its language, to the common intendment of the time, and of those who framed it;) to give also to all parties and authorities, time for reflection and for consideration, whether, under a temperate view of the possible consequences, and especially of the constant obstructions which an equivocal majority must ever expect to meet, they will still prefer the assumption of this power rather than its acceptance from the free will of their constituents; and to preserve peace in the meanwhile, we proceed to make it the duty of our citizens, until the legislature shall otherwise and ultimately decide, to acquiesce under those acts of the federal branch of our government which we have declared to be usurpations, and against which, in point of right, we do protest as null and void, and never to be quoted as precedents of right.
Jefferson also explained his purpose in drafting this resolution quite clearly to several of his closest friends. To William Branch Giles:
Are we then to stand to our arms, with the hot-headed Georgian? No. That must be the last resource, not to be thought of until much longer and greater sufferings. If every infraction of a compact of so many parties is to be resisted at once, as a dissolution of it, none can ever be formed which would last one year. We must have patience and longer endurance then with our brethren while under delusion; give them time for reflection and experience of consequences; keep ourselves in a situation to profit by the chapter of accidents; and separate from our companions only when the sole alternatives left, are the dissolution of our Union with them, or submission to a government without limitation of powers. Between these two evils, when we must make a choice, there can be no hesitation. But in the meanwhile, the States should be watchful to note every material usurpation on their rights; to denounce them as they occur in the most peremptory terms; to protest against them as wrongs to which our present submission shall be considered, not as acknowledgments or precedents of right, but as a temporary yielding to the lesser evil, until their accumulation shall overweigh that of separation
To William F. Gordon (the sponsor of the resolution in Richmond):
"It is but too evident that the branches of our foreign department of govmt. Exve, judiciary and legislative are in combination to usurp the powers of the domestic branch also reserved to the states and consolidate themselves into a single govmt without limitn of powers. I will not trouble you with details of the instances which are threadbare and unheeded. The only question is what is to be done? Shall we give up the ship? No, by heavens, while a hand remains able to keep the deck. Shall we with the hot-headed Georgian, stand at once to our arms? Not yet, nor until the evil, the only greater one than separn, shall be all but upon us, that of living under a government of discretion. Between these alternatives there can be no hesitation."
To James Madison:
I have for some time considered the question of internal improvement as desperate. The torrent of general opinion sets so strongly in favor of it as to be irresistible. And I suppose that even the opposition in Congress will hereafter be feeble and formal, unless something can be done which may give a gleam of encouragement to our friends, or alarm their opponents in their fancied security.
Madison counseled Jefferson to stay the resolution temporarily because he knew of an attempt by Martin van Buren to soften the Adams bill in Congress. Jefferson unfortunately died before the situation resolved and Adams' bill passed the next year. It is plain from the text of his final letters though that Jefferson valued the union and was willing to begrudgingly tolerate is milder "usurpations" in the name of preserving its advantages, but if they became too great to bear he made it perfectly clear that Virginia should separate. His resolution also illustrates that the current strategy of the so-called "nullification" movement today with regard to federal gun laws and the sort is very much in keeping with his constitutional system.
So far as Jefferson may be considered a preeminent, although certainly not uncontested, representative of one major branch of founding-era constitutional theory, Professor Levinson is entirely wrongheaded to dismiss the present so-called "nullification" movement on the grounds that he does.
Jefferson is far from uncontested as a constitutional thinker.
John Quincy Adams was more or less picking up where his father and Washington had left off, before Jefferson took office. His view of what the constitution allowed wasn't so very different from theirs.
They didn't submit an energetic plan of internal improvements to Congress, but given what they did propose, it's hard to say that they would have found such projects unconstitutional.
Jefferson's own party didn't follow his own ideas when it was in power. The National Bank and protective tariffs that he rejected returned under Madison and Monroe. Indeed, Jefferson himself had trouble following his own principles during his own administration. Jefferson the constitutional scholar had real trouble accepting his own Louisiana Purchase and trade embargo.
If you're looking for a break in American constitutional history it wouldn't be when Jefferson's views were rejected or dismissed, because Jefferson's views weren't the only or the most authoritative interpretation of the Constitution. If there was a rupture it happened later.