Not really. Congress has the inherent power to declare a state of war and regulate the military - NOT the President. The president's war-making powers are more emergency in nature; anything beyond that is generally delegated from Congress.
As the CinC the president is charged with immediate action against immediate enemies and enemy targets of opportunity and/or security.
This is no different than the SAME responsibility for force protection that is granted to ANY military commander.
If you recall, the commander of the USS Cole was chastised for NOT properly responding to an enemy who should have been engaged in an otherwise "friendly" (as designated by the State Deptmt) port.
Every commander has that authority of force protection.
This judges wishes to take it from the President.
This judge is insane. I predict she'll be quickly overturned, but I'm no lawyer nor the son of one. I'm just a dumb old country preacher.
There is no need for a declaration of war in order for the president to identify and engage enemies and enemy targets of opportunity/security.
Incidentally, you would find the MILITARY/Strategy/Leadership/Command classes a lot of fun were you ever to enroll in them at a local Rotc.