+1
Larian basically already has this code in their game, in the "Hey, did you just steal from me?" NPC action+dialogue. If you non-lethally down a companion/NPC, next time you're in the area they should come up to you and you get an option to make peace. Persuasion or Intimidation or possibly Deception ("What? No, I certainly didn't attack you. You must be imagining it. Come along now.")
Stretch Goal:
For *important* NPCs (e.g., Minthara), you could interrogate them after knocking them out and essentially capturing them. This'd be another relatively easy fix; just copy Minthara's dialogue from the evil route (e.g., her dialogue from after the goblin party) to that interrogation dialogue.
Double Stretch Goal:
There should be a mid-combat option to ask for peace. E.g., if you accidentally attack or anger someone, this would function as an "oops, my bad" check. It could be a very difficult check, and it should have some limitations like "costs an action to do," "can't just be spammed every turn", and/or "doesn't work on all enemies."
A very detailed system might take into account whether you've non-lethally or lethally incapacitated other combatants. Perhaps: for every enemy defeated, the former would lower the Persuasion DC and the latter would lower the Intimidation DC but also make a failed Intimidation check enrage the enemy leader.