"But it is not possible to give to each department an equal power of self-defense. In republican government, the legislative authority necessarily predominates."
The Federalist No. 78
"This simple view of the matter suggests several important consequences. It proves incontestably, that the judiciary is beyond comparison the weakest of the three departments of power;"
Thank you, Michigander. I was quite sure that the intentions of the founders did not include total equality of powers for the three branches, but could not lay my fingers on any direct evidence of same.
In the context of this article and the sample statement given, the President is simply stating that Congress can make laws against torture 'til they're blue in the face but until amended otherwise, he is the Commander in Chief and the one charged with defense of the nation... and he will use the means necessary to ensure success in his role.