Since Washington's administration a compact theory of the Union, which emphasized the voluntary nature of the Union, had many supporters. even New England was willing to invoke it during the War of 1812. Webster, who so eloquently articulated the idea of a permanent union in 1831, had had quite a different view tin 1813. Lincoln, like Webster a Whig, simply adopted Webster's theory of the Union. in opposition to the Jeffersonian- Calhoun view. Since his side won, that settled the matter, although the lawyers were able to cover up the cracks in the original constitution by means of the 13th and 14th Amendments. Stylistically, the change in view of the country was reflected in the pre-war references that the United States "are," as opposed to 'is" after the war.
The federal government likewise had to turn to the National Guard during Korea, Vietnam, Iraq and probably WWII as well. That doesn't mean that the states are sovereign now. I don't know the exact legal situation of the national guard, but it's not as though the New York National Guard is New York's own army.
Calhoun's theory of government wasn't that of Washington or Marshall. It was quite a questionable theory. Jackson and Madison both rejected it. Most Americans agreed with them in the 1831 nullification crisis. You can find a good overview of constitutional theories here.
The bit about the Civil War changing "the United States are" into "the United States is" is striking, but I'm not sure how solid it is. British usage, and perhaps earlier American usage, requires a use a plural verb for collective nouns. Current US usage doesn't. I don't know all the details, but I wouldn't assume it took a war to change that.
The Civil War did change a lot, but some people assume that everything was the opposite before. If the federal government has power now or if we're one country, they assume the states had to be running things or that we were a loose league of independent states before Lincoln. I'm not sure that's right. The relationship of the federal government and the states and the constitutionality of secession were certainly debateable then. But "debatable" means that people disagreed then, not that the agreed on the opposite of what's accepted now.