Whedon confirmed in some thingy that Book was a spy (cant recall if he was spying on or spying for the Alliance - google would help if you're keen) and that he got stupidly high within the ranks of the Alliance. However he killed a shepherd one day and felt so guilty that he took on that man's identity to remake himself.Daystar Clarion said:Shepherd Book from Firefly.
The guy has an interesting past, there's no doubt about that. Whatever he was, he's deemed important by the Alliance.
I don't think he was always a religious man, but something happened to him, war hero perhaps? Whatever it was, he seeked out religion after the fact. He knows too much to have always been a clergyman.
Lots of hints are dropped throughout Firefly to this of course like his knowledge of guns and Alliance tactics and structure. Most handed clue of course is when Early knocks him out and says to Simon, "Thats no shepherd.".