> life in prison because the President doesn’t like your bosses boss
1. If the President hates the CIA/NSA/FBI director that much they tend to get quickly replaced.
2. Punishing a lower-level agent with prison doesn't seem like an effective way to get revenge on whatever agency leadership the President might hate.
You're making an appeal to a compound scenario: It isn't just (A) "Hollywood ticking bomb" unlikely, but also (B) "TV political backstabbing drama" unlikely, multiplied again by (C) "stupidly baroque form of revenge" unlikely... to get a final probability somewhere near zero-point-zero-zero-not-gonna-happen-LOL.
So no, I don't think that fantastical hypothetical justifies day-to-day erosion of rule-of-law and civil rights.
> Even if you truly believe a catastrophe may happen
If someone truly believes it and they have a reasonable basis behind that belief [0], then surely the morality of saving millions from an atomic fireball or whatever goes pretty dang far in outweighing 1-20 years in federal prison, and they will have ample evidence to make a strong case for getting a pardon.
[0] If spy/agent/analyst dude "truly believes" but for no real reason other than voices in their head, a prophetic dream, hidden scriptures, or alphabet-soup... they are already incompetent and need to be fired immediately to remove them from that position of authority.