They even say that the girl had to die for the sins of the group. Throughout the episode whenever they were accussing one of the group they were sure to show them wearing their crosses.
Sorry for the rant but it's just so noticeable I can't believe I never registered it before
Honestly, it goes back years for this kind of thing. Watched Chuck for the first time a few years ago, and it's kind of amazing just how blatantly the show is federal propaganda. Just unabashedly pro CIA and NSA. And it's weird because you have both Zack Levi and Adam Baldwin, both of whom are right-wing/libertarian adjacent, and it's just shocking how pro-state the show ends up being.
It's nothing new, but once you start noticing things like that, it's hard to not always notice it.
I feel like Chuck is a bit more of a nuanced case. It does present an idealistic view on the alphabet agencies for sure but frequently Chuck runs into situations where his own morality clashes with the government and he frequently becomes disillusioned with them. Several of the shows main villains only became that way because the government ruined their lives and the show doesnt shy away from pointing that out.
That is true, and there's plenty of plot-lines that try to push the "here's this rebel faction of the agency", but it still pushes the idea that these people who are infringing on peoples rights are the outliers and not the main agency.
But you are right that many of the villains are the way they are through the government, and not just some rebel faction.