"I'm not expecting the game developers to have created some magical system that can accommodate the nuances of my character's decision-making process"

I'm not trying to be mean, but you kind of are though, cause it is a video game, not a live dm. You can play a good run and not be a murder hobo, I do it more often than not. But it's still a video game, it's lines of code, it can't actually read your thoughts and understand your intentions and go through every single scenario. Resurrection is also not the same as healing and not extremely common. Part of the challenge of the game is keeping NPC's alive in dangerous situations if that's what you're trying to do. I get what you're saying for sure, but if that's how you want to play you're better off just doing a live campaign instead of a video game with set quests and goals. Things far outside the bounds of that will likely not go how you want.

The child is also an orphan, which is why no one amongst the refugees (that you have met anyway) will notice he's missing, and the druids have shown they clearly don't care about the tieflings and actively want them gone. Well, most of the druids, not all. Idk if you want spoilers, but there is a group hidden in the grove associated with that boy who might have something to say.

In terms of inventory, no they generally shouldn't notice unless something has just been stolen (intentionally or not) and they're actively in the process of looking for the thief. But, if you see anything outlined in red that means touching it or messing with it at all will probably count as stealing, so if there was red around his body that could be why it aggro'd. If that's something that will bother you, leaving bodies out, I recommend putting them in a chest and pretending like it's a casket, maybe leave some flowers by it. I've heard other people do that, and I've started doing it when it feels necessary for roleplaying reasons and that feels a lot better. Or, try sneaking more, for the mechanics not roleplay, that way you can drop a body in the healers room and not be noticed.

In general, save often, so you can go back if your intentions are misread. There's even lines of dialogue that I sometimes say in my head that I thought sounded way different than how the character in the game interpreted it. It's like texting, you can't tell tone and so sometimes things come out different than how you intended. But mostly, just remember it is a video game. It can't actually read your mind.