Jamie’s been walking a tight rope trying to find the right balance of loyalty to the crown and what he knows about history. Murtagh wanting to fight doesn’t help but Jamie goes along trying to influence and assist when he can. However, Knox’s inquiry into Ardsmuir forces Jamie’s hand.
After Jamie is discovered to be a Rebel by Knox, Jamie strangles him to protect Murtagh and the others. Jamie hides the evidence by burning the Ardsmuir prison roll and starting a fire which destroys all the evidence as to his actions.