This is a very good point. Games such as Dishonoured have it so you can actually go through the game without killing anyone - quite a feat considering you're an assassin and there are several plot-based assassination targets. Stealth games often have this kind of thing, but it's rare in RPGs, as the OP said. Skyrim had a perfunctory surrender mechanism but (a) it rarely triggered and (b) true to Bethesda's form, it glitched when it did trigger, usually, with the enemy suddenly attacking you again right after they'd surrendered and forcing you to finish them off.
One way loot could still work with this is that the enemy offers you money or items to not kill them. They'd say "I yield, please - don't kill me! Take this!" and then drop their gold and run away. Something like that. They wouldn't always do it, perhaps, which would make sparing people less profitable than killing them. There could also be weapons that merely knock people unconscious, like a truncheon, and then the player can search the body for items.
