I'm guessing that internal sovereignty would include the right to peacefully remain in the Union without concern the other states would try to remove, restrict, or otherwise encroach on her territory.
Yes, among other things. N-S's #262 is a tour-de-force concerning some of the issues of external vs. internal sovereignty. We need to keep in mind that Madison, the chief architect of the Constitution, described the form of government developed at the Philadelphia Convention as being without historical precedent. The new constitutional form of government did not fit nicely into theories of sovereignty that were understood in those days.