The President is never entirely free to choose his foreign policy team, but Obama has a great deal of latitude for the second term:
The upshot is that the Obama administration begins its second term with much greater foreign policy freedom of action, whether in domestic, strategic, or bureaucratic terms. If Obama wants to follow through on the “pivot” to Asia, he should have the freedom to do so. The first year of the second term should demonstrate how seriously Obama intends to pursue a redistribution of military and diplomatic effort towards Asia. An early indicator will be who the president taps to replace Petraeus at CIA, as well as how the administration handles sequestration. For those either anticipating or dreading a larger U.S. commitment to Asia, uncertainty shouldn’t last long.
One way of interpreting the attention paid to the Benghazi imbroglio is as an effort to cripple the second term team.