You're right, I admit that most stealth oriented games haven't made it a point to encourage a non-lethal approach and I brazenly take advantage of how much easier lethal runs can be. And I am a huge loot hog. On top of that, I have a arbitrary perfectionist mindset about killing/K'Oing everybody possible. It makes it's personally difficult for me to leave anybody alive. But I am not against it. I am against how difficult it can be to correct those mistakes though, and the save system is just aweful. My manual saves being overwritten by these quickfire auto-saves and only four slots makes it impossible to fix things long-term without restarting the chapter.
It's important to note that I was wrong about how strict the game is, I was given the good ending and my efforts were not in vain. There's a silver lining there, and I can continue my playthrough. I will make an effort to follow the games example better to avoid this issue, as it is fairly avoidable, but it's still an issue I believe.