There's a clash going on in this novel between two different models of government. One is the Lowland style, which is based on the idea of Scotland as a unified nation with a single ruler. The second is the Highland mode, with lots of different mini-countries organized by family clan. Each of these clans naturally have their own allies and enemies, so Alan's clan, the Stewarts, are equally opposed to the English king and to their fellow Highlanders who happen to be members of the Campbell family. Blood obligations are incredibly strong under this clan system. When Davie and Alan both agree to allow James Stewart to set out a reward for their capture (in order to deflect suspicion away from himself), Mrs. Stewart hugs Davie and thanks him. But to Alan, she just says, "As for you, Alan, it was no more than your bounden duty" (19.41). In other words, even though Alan's taking a huge risk for James's sake, his wife sees this as nothing more than the expected duty of a family member.
Davie's ignorance about his own family tree serves as a foil for Alan's more traditional, clan-based loyalties.
The Stewart allegiance with the Camerons forces Alan to keep silent about who the murderer of Colin Roy really is, even though alerting the authorities would clear him and his family of suspicion.