Fleeing is not an option.
Yes, it is. You complain about unreasonable NPC reactions, but the player
has to kill much weaker NPCs, because 'they started it' or they could hold a grudge than might possibly cause some inconvenience?
No. As demonstrated by my example, fleeing is a non- resolution. You rightly identified that once meeting the NPC again, they should continue trying to resolve the issue. As discussed, the murder is not a reasonable resolution to "You stole my wooden spoon", yet it is essentially the only resolution available to them.
You know, she could simply take her wooden spoon back and then refuse to talk to you again.
You mean like already exists in D:OS, depending on the situation, NPC and (primarily) your reputation?
Isn't that the point? The system's there. Why can't they use it?