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
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.
The government gives Casey the green light to kill Chuck if he has to after they are working together IIRC. In the first couple of episodes too.
Yep, IIRC this is a continuous plot thread for the entire first season that they want to kill Chuck as soon as they rebuild the Intersect. There is also the constant threat that they may find it too dangerous to continue letting him live normally and may lock him up somewhere for protection during the first few seasons. Later plotlines reveal that the government is directly responsible for the events that led to Chuck's family falling apart. The show even subtly slipped in a few "are we the baddies?" moments where Chuck is forced to make choices that don't sit well with him.
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.