People who you knock out should not be hostile to you upon waking up. That defeats the entire purpose of knocking them out and makes it objectively worse to knock people out instead of just killing them (I too, had this aggro'd-NPC-in-the-goblin-camp experience)
A compromise between reality (it's not like knocking them out magically makes them like you) and knocking out being actually useful is to have them talk to you! This could work similar to the "hey, there's a thief around, is it you?" dialogues, where you have an option to persuade/intimidate the NPC into staying non-hostile.