Bush couldn't have "cleaned them out" because there is a law protecting non-political appointees from being fired. That's called the Civil Service Law.
Over the years, agencies like State, DOJ, and EPA have become increasingly liberal, because conservative employees tend to migrate to the private sector, while the liberals become more entrenched and move up higher in the chain, getting more authority and influence.
It is a problem any Republican president will face, and it is one that Reagan faced as well. The only way I can see solving this is to radically reduce the size of some of the departments and/or combine them, while allowing no new hires and getting as many people to retire as possible. This, of course, would be heavily resisted by the employees union.
And even then, how many conservative scientists are you going to get in EPA? Anyone worth his salt is going to work for corporations, not the government.
Adding I was talking about scientists, not diplomats. State is about the only place people can go if they are interested in a diplomatic career.
Which is why we should all be backing DeMint in his trying to block this guy Obama wants at TSA since the guy will not state emphatically he will not unionize the TSA... an agency that should not be under any circumstances given union protections... JMHO
Bottom line we are not corrupt they are.