The 11th refuted the justices arguments - they did not go unchallenged. Then nor now:
[W]e have understood the Eleventh Amendment to stand not so much for what it says, but for the presupposition of our constitutional structure which it confirms: that the States entered the federal system with their sovereignty intact; that the judicial authority in Article III is limited by this sovereignty."
Justice Scalia,Blatchford v. Native Village Of Noatak, 501 U.S. 775 (1991)
For an excellent discourse on the 11th and state sovereignty see Alden et al. v. Maine, 527 US 706, (1999).
The 11th does not refute Chief Justice Jay and Justice Wilson. It doesn't even address what they say.
Wilson:
"As to the purposes of the Union, therefore, Georgia is not a sovereign state..."
Jay:
"By this great compact however, many prerogatives were transferred to the national Government, such as those of making war and peace, contracting alliances, coining money, etc."
The 11th amendment says nothing about any of that.
The 11th amendmet says:
"The Judicial power of the United States shall not be construed to extend to any suit in law or equity, commenced or prosecuted against one of the United States by Citizens of another State, or by Citizens or Subjects of any Foreign State."
You'll just say anything, won't you?
Walt