I know that at the operational level the deputy (S or O) does NOT tell the Cdr what to do or how to do. That's a great way to have a short walk into oblivion.
At the NCA level, though, all bets are off. I don't know how those folks live in that rarified air. For all I know, Rummie's pulling ALL the strings. I hope not, because, even if he's a good guy, he's not a battlefield expert.
Our worst wars have been those where politicos pulled operational strings. The absolutely should be deciding broad objectives, but they shouldn't be telling the experts how to suck individual eggs.