Shooting the fulcrum baddie was pretty much required to protect him. Lying to Chuck's face about it probably hurt the most. I think they should have had her be straight about it to him. Tell him that he had to die or he and his sister would be in grave danger. By doing it this way, the writers killed the spark for her in him that was growing again...
Still a great season. Since we are in reruns, I have to rewatch "Chuck vs. Tom Sawyer"... the Missile Command episode for those that don't recognize the title..... IMHO the best episode of the show ever...