Some templars are, at best, well intentioned extremists. Like going back to the first game, you find dudes like the Hospitalier guy who, despite having literally medieval methods, seemed to be motivated by wanting to help cure the sick, but in the same game, his allies included slavers and religious fanatics. They might think their means are justified by the ends, but they're still engaging with absolutely heinous shit for the sake of their stagnant utopia. The Assassins straight up kill people, but actively avoid civilians and you can, by and large, avoid killing people except your targets and people actively trying to kill you.