President Obama made a brilliant move giving up Rice for Secratary of State. He can now move her to National Security Advisor, much how Nixon originally had Kissinger inside the White House. As National Security Advisor, she is covered by Executive Privilege (Secretary of State is not). This positioning affords Obama a great deal more strategic range. Kerry in State plays into placating Republican Senators - they will resist attacking Kerry. Kerry is ultimately an ineffective leader (also known as "Figure Head"), so he can travel the world collecting frequent flyer miles without disrupting the President's Foreign Policy Agenda. Loss of Kerry seat allows for some drama that will take news cycles away from Benghazi et. al. State Department then just becomes a shield of activity for Obama to do whatever he wants foreign policy wise behind wall of White House.
A grand Irony of course is that Benghazi actually dropped into the lap of the National Security Advisor. So if a similar event occurs in the future, Rice will lead the real time response.