Fantastic episode. I don't think you noticed that this one also had a different tagline just like the season one finale. That one said "Trust No One", and this one said "Deny Everything". Regarding your reaction/analysis, you are doing it as good as always, I just won't say anything about when you go really in depth, in order to avoid spoilers. However, you might just be forgetting one thing regarding past events. When you think about when the decision might've come to take/do something about Scully, don't forget the last scene from episode "Sleepless", what Krycek says to Cigarette-Smoking-Man in that office, and what CSM replies: "Scully's a problem"... "Every problem has a solution".