I guess you missed the word "weapon".
A commander in chief doesn't mean authorization to just shoot at anyone.
So according to you, Commander-in-Chief doesn't get to command.
How do you feel about Jefferson firing on the Barbary States without Congress declaring war? Or Lincoln invading Virginia without Congress declaring war? Or Wilson invading Mexico without a declaration of war? Or FDR firing on the French without a declaration of war?
In each of these cases, the President was acting as the commander-in-chief of the military forces, which is his Constitutional duty. And in no way shape or form is that duty rendered void without such Congressional action. Our founding fathers never intended for a President to be denied his Constitutional authority because of a weak vacillating Legislature.