There is nothing illegal, nor immoral, about firing the political appointees of your opponent.
It is the easiest and most effective means of changing the nature of political institutions to share your own political vision.
It is extremely foolish not to do so because you are left with a cadre of embedded opponents who will do everything within their power to make Bush policies ineffective, and make Bush look foolish or even set Bush up with legal liabilities if at all possible.
The CIA is institutionally hostile to Bush. That needn't have been so.
The State department is institutionally hostile to Bush. That needn't have been so.
The Attorney general's office and the FBI are institutionally hostile to Bush.
The government is run by these people. It is not run by President Bush.
I agree with your diagnosis of the situation, but I think that there are relatively few "political appointee" positions at the top of each department. Then there are all sorts of career civil service positions which are called "Senior Executive Service" as I recall.
Perhaps Bush could have replaced more people, but I think the vast majority of federal civilian positions are subject to the strictures of civil service regulations. Career people who go into State and CIA in recent decades must be predominantly liberal to begin with - I've known several who were/are ultra-liberal, and I've never known a single conservative to express much interest in a career with State (though some in CIA). It's a very intractable problem....
No.
Of course the CIA is hostile to President Bush, but you can't just fire the 2,000 top Leftists overnight. You've got to do what GWB has been doing which is to create a new intel agency on the one hand while purging the CIA on the other...knowing that GWB is going to come under fire from those thousands of career spook Leftists and that it will take extreme courage and patience to beat them.
They don't run the government. They do influence it. If they actually ran the government behind the scenes, Governor Bush would have never won in 2000.
Same goes for the State Department on an almost as serious scale.
The Attorney General's Office is the one area where President Bush could have been more brash, but that would have been a temporary fix...what the Bush Administration is doing inside the AG's Office will lessen the long-term bias against us...that's preferable to a short-term-only fix even if we have to suffer more in the meantime.
As for the FBI, I'd rate it as biased against us, but not openly hostile...certainly not at the level of the State Department and CIA. It's the one area of government more suited for liberals, anyway, if such a thing is possible.