With most acronyms, you have to think about how they fit into your speech. If you feel that the acronym is actually replacing the words it stands for, then use, or don't use articles as you would if you were saying the name in full.
"CIA" is a proper noun - it is the name of a government agency. You would normally say "the Central Intelligence Agency", so you should use the same article with the abbreviation:
- I work for the CIA.
- I work for the Central Intelligence Agency.
Sometimes though, we use nouns as adjectives - for example, "car door", where "car" which is a noun is acting as an adjective for the noun "door".
When "CIA" is used as an adjective, such as in "CIA Officers", or "CIA Troops", you would use the article appropriate to the subject noun, or not at all, for example:
- CIA officers hammered at the door (no article needed)
- A CIA officer hammered at my door (article needed for "officer")
I can't really explain why the above has not been applied in Tom Clancy's novel, except that the author is known for his high level of technical detail in his novels. It may be that referring to agencies in an abbreviated form is common within related government agencies. If that is the case, like a lot of terminology, the rules of grammar do not always strictly apply.