Not at all, because as I pointed out, there are two separate issues:
Issue #1: How the right is defined by the Constitution.
Issue #2: Who is prohibited by the Constitution from violating it.
Thomas was commenting on Issue #1. He had nothing to say in regard to Issue #2.
Justice Thomas: "[P]erhaps, at some future date, this Court will have the opportunity to determine whether Justice Story was correct when he wrote that the right to keep and bear arms 'has justly been considered, as the palladium of the liberties of a republic."'
Here is Justice Story's quote: "The right of the citizens to keep and bear arms has justly been considered, as the palladium of the liberties of a republic;"
If Justice Thomas considers the RKBA the key liberty of a republic, then why would he think that the States could violate it and still remain republics? It is his job to guarantee that States have republican governments.
He didn't say that he did.
He said, ""[P]erhaps, at some future date, this Court will have the opportunity to determine whether Justice Story was correct."
If you're referring to the provision that "The United States shall guarantee to each state a republican form of government", then first of all, that clause does not vest that obligation in the judiciary specifically, and secondly, the form of government is not what's at issue here. Gun control, however inexcusable it is, does not of itself alter a state's form of government any.
That clause was not put into the Constitution so that federal courts could endlessly second-guess state laws based on purely vague criteria. The people never would have ratified the Constitution if that had been the case.