Yes, something like that note is more or less exactly what I'd expect SCOTUS' position to be. And I don't think it would be a close decision.
Then the question becomes, if Congress endorses the pact, could it go into effect? The success of an equal protection claim against the agreement is a little trickier to forecast, since the justices who typically support a broad reading of equal protection are likely to be the most sympathetic to arguments for eliminating the disparity between the popular vote and the EC. But I think the Court would see NPVIC, rightly, as an "end run" around the amendment process, and require that state elections remain state elections: States do not have the power to facilitate national or interstate plebiscites outside the usual Constitutional order.