Ack! I had a moment of panic that he was about to let him on the ship, too. But I realized in a second that that wasn't going to happen because...well, because he's not Jayne. He's not Book. He's something in between the two that makes him irreconcilable with Mal's beliefs. He's a man of faith in violence instead of just a man of violence or a man of faith. Plus, the Operative got his people killed, and I don't think that's something Mal's ever going to forgive him or himself for (which ties in with my understanding of why he kept the others on originally, was that, yes, useful, but also they proved willing to save the lives of his crew).