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 always interpreted that though as a difference of personality/political gamesmanship more than ideology or substantive policy concerns.