The Trials & Treasure core book does a lot of good work on different player motivations and how to avoid (if you wish to) a murderhobo style of game play. I feel a couple of tweaks to the Memories of Holdenshire adventure could reinforce this.
Players potentially will kill some or all of the Guards during their escape from the city, as page 24 has the guards trying to fight to the death unless outdistanced etc. Of course the Players might come up with non-lethal ways, but there is nothing specifically encouraging the Narrator to think about that. First i think this would be a good point to use the Bloodied mechanic in a different capacity, with a guard retreating if Bloodied. This gives an idea to the Narrator/players that not all combats need to end in death. Secondly, on page 23 of the pdf I would have Belton say: "Take the reins! We've got to get way but don't kill anyone!" This helps with 1 but also implies consequences if they do kill a guard. Thirdly, I personally would place a sack of cabbages in the wagon as ammunition to throw at the mounted guards to knock them off .
At the conclusion of the campaign page 50 only talks about being forgiven for the mistaken identity/involvement in the death of the sister. The party gets a reward and offer of a celebratory dinner. It does not cover any consequences of killings of (innocent) guards during the escape or later that might have happened - remember this would have occurred when the party is in control of its own actions, albeit wanted criminals. A sentence or two added here could provide the Narrator with some thoughts on consequences: the Captain agrees to forgive the crimes as after effects of the mind control and says he will support the family of the dead guard; the party is in debt to the families; a relation of the guard will come seeking revenge; or the guards weren't actually dead, they were unconscious and later healed.