'(It's) appropriate for the head of such department or agency [read: CIA] to direct the operations of the element providing that military support while working with the Secretary of Defense.' A 'significant advantage of doing so,' he continued, 'is that it permits the robust operational capability of the U.S. Armed Forces to be applied when needed.'
That’s contentious: it would put the military in the territory of performing operations that the government can legally deny all knowledge of ordering... (Source)