Exactly---and that is why Sec. Rice needs to do some housecleaning like Bolton does in the UN....
The State Dept. and the CIA have been none to supportive and cooperative with President Bush these last 4-5 years, and I think that now that Bush doesn't have to worry about winning another election, he isn't going to care whose feelings he hurts, or whose feelings people like John Bolton hurt....
House cleaning won't work. You are not going to change the corporate culture overnight. Influential bureacracies like the State Department, CIA, and DOD have developed ways to deal with their political appointee masters. Ultimately, they can wait them out. But there are other ways to thwart or change policies the institution doesn't agree with.