Pacifism =/= being the goodest girl who ever did do good, even if that's how most games/stories portray it as. It just means not killing. Some deaths are worse than others and death is debatably not even the worst thing that can happen to someone.There is a bug with glossary. Having finished the game when you load an old save the inquisitor and his son already have a line about their fate in the end
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For instance, the guy your talking about was dying of an abdominal wound which would take a while for him to die of and in pain all the while. With his corpse being left for the beasts. The mercy kill and honoring of his last request for his body to not feed the beasts is a bit morally complex and feeds some of your darkness to gain some strength from it but it is balanced out by asking the man if he wants it. Thus 1 darkness and 1 balance. Also you get 2 darkness if you don't even engage in conversation with him and 1 humanity for talking to him to get to the choice between just killing him or offering the mercy kill.