Whether we're at war or not has nothing to do with it (except insofar as you take the Bush Administration's argument that AUMF implicitly granted wide-ranging foreign espionage authorization under FISA). As tptacek pointed out, my argument is fairly banal and
should be uncontroversial: If a law can be interpreted in any way that avoids usurping Executive authority, the Executive can and should interpret it that way. This is not dissimilar from the Judiciary's general practice to read Congressional statutes as constitutional if there's any such plausible reading.
If Congress passed (over a veto) a law tomorrow requiring the President to fire his Secretary of State, that law would be unconstitutional. The President wouldn't need to wait for the Supreme Court to overturn it, he could simply refuse to obey it, and he would be right. That has nothing to do with John Yoo or whether or not we're at war.
(A similar issue actually came up during Reconstruction: The Tenure of Office Act was unconstitutional, and Johnson was right to violate it, though it got him impeached.)