It was the president's decision and his alone. It wasn't a vote. Her tenure as SOS was confined to flying around gladhanding, stupid shit like the Russian reset button, and pushing the TPP. More serious and capable people handled Afghanistan, Iraq, and the ME in general. SOS Kerry was trusted with that authority and hit the ground running.
Finally, not being honest about supporting HRC when it's so effing obvious is the very essence of hypocrisy and you're soaking in it.