He points out that the storyline in the movie 'Serenity' includes a character known as 'The Operative' who was introduced to 'the true background of the reavers' and as a consequence 'relinquished his role as an Operative'.
Commenting on the theory that Book had served as an Operative he says:
'It is possible a similar experience happened to Book. It is possible he went through something that forced him to see the errors of whom he served, and left to become a shepherd, or at least to pose as one.'
Certainly Book 'wasn't born a Shepherd' and presumably must have been through some sort of conversion experience.