Know what I think? I think Shepherd Book was an Alliance Operative.
Further, I think that he was at Serenity Valley and that HE falsified the order to Mal to lay down arms (Hey, they were holding their own, and reinforcements would have kept to battle going. Serenity Vally’s strategic importance is a critical plot point several times in the show. The Browncoats wouldn’t have just abandoned it. I think the Alliance compromised the Browncoat’s communications and told the people on Serenity to surrender…and told the rebel command and control that the battle was lost.
Then, Book had a crisis of faith like the Operative in Serenity the movie, and went to the Abby to get his head on straight.
Then, he saw Serenity, and took it as a sign that this is where he was supposed to be…to go back out into the world and do good…and he found a way to atone for his sin…and the atonement that he decided upon eventually was helping Mal to restore his faith.
I don’t know, if I was writing it…that’s what I would do.