One thing I caught last week (or was it 2 weeks?) when I watched "Serenity" was Book's reaction at the end of the episode. Book is noticeably disturbed, as any good religious Shepherd would be, at the killing of the Fed agent and how Mal and the crew live just outside the law. Yet, later, we'll learn that Book wasn't always a noble religious shepherd. He's had a dark life. The later fleshing out of his character kinda contradicts this scene in "Serenity." Book shouldn't be having a crisis of conscience.
Of course, he could be acting in order to preserve his cover.
SPOILERS BELOW -- DON'T READ IF YOU HAVEN'T SEEN THE SERIES YET.
I think it makes sense, but that's based off of how I saw things. I thought that Shepherd Book was a religious man that really did serve in an abbey, but this happened after a life that probably put him there to protect himself and others. You have other hints that he's more than meets the eye when he's injured and has Mal give his id to the Alliance, and they get him the best medical care possible with a lightening speed.
Then, you have Early saying that Book isn't really a Shepherd in the last episode, like he knows something about his past. This doesn't mean that when Book was at the abbey that he really didn't "serve" and find a spiritual path for himself. Who knows how long he was there and why? This was the number one reason why I wished the series had continued, but alas, it wasn't meant to be.