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
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.