I think that Joss Whedon is really doing that on purpose. He does a great job of making the characters real, and in real life, sometimes we never really know someone. I still like to think that Book is a retired Operative. Just a thought.
If such is the case, are we sure Book is even dead. That gut wound didn't look to bad, I doubt that Mal took Book's body with them to Marand (Planet) and there are ways to fake a person's death to the point where even the doctors are fooled.