If I understand, Jefferson was conerned about certain DECISIONS, as you say. Here we have a Supreme entering the public fray in free discourse, which is entirely outside the scope of her charter. To me, this does not bode well.
In denying the right they usurp of exclusively explaining the constitution, I go further than you do, if I understand rightly your quotation from the Federalist, of an opinion that “the judiciary is the last resort in relation to the other departments of the government, but not in relation to the rights of the parties to the compact under which the judiciary is derived.”Whatever about Jefferson’s opinion may be correct or incorrect, he was certainly prescient.
If this opinion be sound, then indeed is our constitution a complete felo de se (suicide pact). For intending to establish three departments, coordinate and independent, that they might check and balance one another, it has given, according to this opinion, to one of them alone, the right to prescribe rules for the government of the others, and to that one too, which is unelected by and independent of the nation. […]
The constitution, on this hypothesis, is a mere thing of wax in the hands of the judiciary, which they may twist and shape into any form they please. It should be remembered, as an axiom of eternal truth in politics, that whatever power in any government is independent is absolute also; in theory only, at first, while the spirit of the people is up, but in practice, as fast as that relaxes. Independence can be trusted nowhere but with the people in mass. They are inherently independent of all but moral law. …