It is the Bush State Department.
If the Bush Admin doesn't have control of it, they don't need to be trying to run the Executive Branch.
Bush is now in his 2nd term. It is the Bush State Department. Any trouble-making Clinton hold-overs ARE Bush's fault, now.
You don't understand the civil service system very well. This guy was low on the totem pole, and very likely is covered by civil service regulations. Only the higher ups can be replaced when administrations change. Generally, in other departments, that's a mostly good thing, as it provides for some level of expertise and continuity. But at state, which needs to be even more attuned to the current Administration than even DoD, it does cause some major difficulties.