Joseph Gordon-Levitt did an excellent job this episode in playing a sort of "Charlie-gone-wrong" type of character. Scott was who Charlie might have been had he not had the support he has and had he been put in trying circumstances without that support system.
Of course, the dead guy Hoke also serves as a "Charlie-gone-wrong" example. He is what Charlie might become if he only thought of the numbers and not of the real-life situations and exceptions. Once again Charlie is saved from this fate by his support system. Larry and Don will never let him forget the real-life factors.
So Charlie is left thinking about how much harm his work for the NSA has caused. A valid concern, if simply so that in the future he knows to ask. The episode does a great job of showing Charlie that not everything is black and white.