Maybe we should start analyzing the first term? Far as I know the president has a say when the country is being challenged by a foreign power. More so, I think we all know what relationship the SOS and the POTUS had back then. Probably hasn't changed much, but in times like this I guess principles aren't worth the effort. Obama sidelined her effectively and he centralized foreign policy like Nixon.
I've read different, but am open to being proven wrong. Especially given the antagonism between the Clintons and the Obamas.
I've always interpreted that though as a difference of personality/political gamesmanship more than ideology or substantive policy concerns.