This article isn't about that, though? USAID was never designated as an independent agency. But it was a statutory agency, which means that the President was required to run it according to its statutory structure.

Congress still directs the President, for example, to operate a Food and Drug Administration in coordination with the HHS secretary and the commissioner of food and drugs. All three of them have broad authority to direct its operations and efforts as they see fit. But they may not decide to stop regulating food and drugs entirely, nor recruit a toadie from Elon Musk as a sin-eater to make that decision.