There is no way that Sotomayor genuinely believes this. If Trump becomes president and is prosecuted again, I guarantee she'll argue that his crimes don't fall under the President's official duties.
(In a previous version of my comment, I thought that the previous commenter was referring to the Foreign Emoluments Clause and cluelessly asked whether there was a domestic version.)
They would if you had used your company credit card to pay a hitman though. Perhaps this isn't the strongest argument for why the military for a political assassination isn't an official act. My point still stands though that all limitations of the powers of the President are still there, so not everything they do will be considered an official act.