One MonkeyOne Monkey and ShanShan are right, that there are tons of novels/movies where entities like the CIA are the bad guys. Unlikely that someone will sue you, or even can. Right of free expression and stuff like that.
But, because both gave the advice "write what you like and only care about the individuals", I have to step in. That could be bad advice. Especially if you leave governmental entities behind, heading towards companies and trademarks.
Well, guess what, IANAL. But there is a lawyer out there, writing about the trademark topic. This is off-topic to your question, so I keep it short:
Disparagement means to place the product or service in a “bad light”. You should not disparage a product or service unless you are writing a non-fiction critical evaluation of the product or service.