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
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.