Yes, the President is the CIC and is at the top of the chain of command. But the President doesn’t run the entire Department of Defense any more than he runs the Department of Justice, Treasury, or Homeland Security.
Congress grants specific authority to the heads of the various Executive departments/agencies. Not every decision those department heads make comes from Obama. They require the authority to run their department. Special circumstances may require Presidential approval and the ultimate responsibility for all decisions may rest with Obama, but that doesn’t mean that every decision they make is illegal because they work for Obama.
If you cannot accept that basic premise, then yes, any further discussion is a waste of your time and mine.
Overview of the US National Security Structure
The National Command Authorities (NCA) are the President and Secretary of Defense together with their duly deputized alternates or successors. The term NCA is used to signify constitutional authority to direct the Armed Forces in their execution of military action. Both inter-theater movement of troops and execution of military action must be directed by the NCA. By law, no one else in the chain of command has the authority to take such action.
He [the SECDEF] has nearly plenary (full; complete; entire; absolute; unqualified) authority, direction, and control of the entire department [of Defense].