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Not true. Simple servants can be fired, it's just not easy to fire them. However, the key piece that you might have missed is that Bush RE-APPOINTED many of these people to new terms. At their level of service, they serve a fixed term that expires unless the president re-appoints them to another fixed term. This is different from the normal simple servant who can be fired for any reason within their first year; after they have completed their first year it is extremely difficult to fire them, but it is possible.

Typically, when one administration leaves and another one comes in, it is traditional for all of the bureaucrats serving in appointed positions (such as Clarke and Tenet) to resign their positions so that the incoming president can select his own appointees. I don't know if this tradition (protocol) was observed with these appointees or not. The incoming president has the option of accepting the resignations or rejecting them. The fact still remains that in 2002, according to the article, Bush re-appointed Clarke. So, if he wanted to get rid of him, he had his golden opportunity. He chose not to take it.