The current way NPCs that are allied to one another is a little odd. Let me give you a situation to demonstrate what I mean and what I'm suggesting.
You have + with the Blue Dwarves, and - with Durin's Folk. There's a Blue Dwarf and a Dwarf in a room. You kill the Dwarf, which is allied with Blue Dwarves, but the Blue dwarf will not retaliate and attack. That generally makes no sense; if your ally or brethren were killed in front of you, you would take action, whether they have a little bit of a good reputation in your people or not. What im suggesting is that that a faction sees their ally killed in front of them, they will take action, regardless if the player is neutral or positive with them. It just makes more sense.
Thank you for reading and have a wonderful day!