I was rewatching Serenity the other morning and got to the scene where Mal and Book are talking up on that hill while Jayne, Kaylee, etc are down by the fire. I don't have an exact transcript of what Book says but it's something like "that means an operative, trouble you'd not know." That moment made me wonder, was Book maybe an operative? He seems to know a bit about what the Alliance will send, strange. He goes on and on about belief, and when he's dying tells Mal that he doesn't care what Mal belives, just that he does. And what is the operative in the BDM all about (besides killing River)? Belief. Even Inara notices it. And int he end when his belief is destroyed he's says he's "no longer their (the alliance's) man" In Safe the crew asks: Where could someone get an ident card which would get them immediate medical treatment? (or something like that), an operative would have that, even an ex-operative. Book has unusual knowledge of weaponry, etc (as noted several times, War Stories especially). Could it be that he was an operative and somehow got out of it and became a Shepherd?
Perhaps this has already been discussed, and I should say that Book is hardly my favorite or most studied character, but I'd love to hear some comment. Though it's certainly not the only explination, it's an interesting one.