The people have rights, but the people speak as their respective State. Who are the States, are they not the people that inhabit them?
On examining the first relation, it appears, on one hand, that the Constitution is to be founded on the assent and ratification of the people of America, given by deputies elected for the special purpose; but, on the other, that this assent and ratification is to be given by the people, not as individuals composing one entire nation, but as composing the distinct and independent States to which they respectively belong. It is to be the assent and ratification of the several States, derived from the supreme authority in each State, the authority of the people themselves. The act, therefore, establishing the Constitution, will not be a national, but a federal act.Madison
Taylor wasn't really concerned with the words of the Constitution or with the way it worked in practice. He was imposing a something like a geometrical proof on the Constitution, looking for a center of absolute sovereignty in a system where sovereignty is limited and conflicting authorities are checked by and balanced against each other. If you're looking for absolute sovereignty in a system you'll probably find it somewhere simply because you think it has to be there, but that doesn't mean it is there or that other observers will agree with you.
It would be interesting to hear your definition of a Republican form of government. Did all the participants of the Virginia Ratification Convention have it wrong? No. They only corroborate what John Taylor said:
We have heard that there is a great deal of bribery practised in the House of Commons, in England, and that many of the members raise themselves to preferments by selling the rights of the whole of the people. But, sir, the tenth part of that body cannot continue oppression on the rest of the people. English liberty is, in this case, on a firmer foundation than American liberty. It will be easily contrived to procure the opposition of one tenth of the people to any alteration, however judicious. The honorable gentleman who presides told us that, to prevent abuses in our government, we will assemble in Convention, recall our delegated powers, and punish our servants for abusing the trust reposed in them. O sir, we should have fine times, indeed, if, to punish tyrants, it were only sufficient to assemble the people! Your arms, wherewith you could defend yourselves, are gone; and you have no longer an aristocratical, no longer a democratical spirit. Did you ever read of any revolution in a nation, brought about by the punishment of those in power, inflicted by those who had no power at all? You read of a riot act in a country which is called one of the freest in the world, where a few neighbors cannot assemble without the risk of being shot by a hired soldiery, the engines of despotism. We may see such an act in America.
That wasn't John Taylor.
Surely the people are also part of the country as a whole. Do the decisions that we make as a country count for nothing? Are we simply a loose alliance of states, that any state can walk out on at any time for any reason or no reason? Even before the Civil War it was clear that that wasn't the case.
That Madison quote is from Federalist 39, where he discusses the mixed character of our Constitution, which is neither wholly federal nor wholly national. You don't get a clear-cut argument for secession or nullification or state sovereignty from it, as Madison own views when the country faced those questions in the 1830s indicates.
Your other quote is from Patrick Henry who was also an Anti-Federalist at the time and voted against the Constitution. Surprisingly, ten years later he was a Federalist and an opponent of the Virginia and Kentucky resolutions. The French Revolution had changed his mind about political upheavals.
In 1798 he argued that Virginia “had quitted the sphere in which she had been placed by the Constitution, and, in daring to pronounce upon the validity of federal laws, had gone out of her jurisdiction in a manner not warranted by any authority, and in the highest degree alarming to every considerate man; that such opposition, on the part of Virginia, to the acts of the general government, must beget their enforcement by military power; that this would probably produce civil war, civil war foreign alliances, and that foreign alliances must necessarily end in subjugation to the powers called in.” So Patrick Henry recognized other threats to the country than those he saw in 1788.
As regards your quote, it sounds like Henry's talking about how difficult it can be to overthrow a tyrannical government without existing local or state political institutions. He's right. It took a lot of effort to get the American Revolution underway, even with the existence of provincial assemblies. But it can also be too easy for states or localities to break away from an existing government that isn't in any way tyrannical, and that's something that Patrick Henry also came to understand.