In the case of the warrantless wire taps the will of Congress is expressed clearly in Foreign Intelligence Surveillance Act (FISA). Those who argue that the President's powers as Commander-in-Chief gives him the authority to ignore these express wishes of Congress are in fact arguing for military dictatorship.
One of the fundamental principles of all political systems which seek to avoid military dictatorship is that the military power should be subject to control of the civilian authority, and history tells us that such control must be absolute - no matter how grave the military might consider the threat, no matter how unwise they might consider the politicians, they don't get to decide when, why or against whom we go to war or what is and isn't acceptable behaviour in the prosecution of war once declared.
The US Constitution deliberately establishes a system of government in which the President administers the laws enacted by Congress. It seems the "absolute powers Commander-in-Chief" groupies believe that the President is not constrained by that Constitutional system. If it looks like a dictatorship, and sounds like a dictatorship, and acts like a dictatorship, chances are it's a dictatorship.