It makes sense, in a novel focusing at least in part on a murder, that there would be a lot of talk about morality. But somehow these discussions never seem to go very far in Kidnapped. Consider Alan and James Stewart's conviction that it would be better for them to take the blame for the murder – even though they're innocent – than to fink on the real culprit (a Cameron from Mamore). (Davie thinks this is dumb, by the way.) Or there's the moment when Davie jumps all over Cluny Macpherson for gambling at cards, showing the signs of his relatively puritanical religious upbringing. In both of these cases, there are clear disagreements over the right thing to do, and neither side manages to persuade the other. So they just move on. Morality is a bit like politics in the book: there's a lot of talk about Jacobites and Whigs and so on, but none of these political ideas is ever given any meaningful substance. Similarly, there are good and bad men in Kidnapped, but there doesn't seem to be any rule about who will do the right thing when.
Stevenson uses hypocritical characters like Captain Hoseason and the blind catechist Duncan Mackeigh to imply that praying or going to church is no proof that you are a good person.
Stevenson refrains from making definite moral judgments about his characters.