1. Add menu option ''Set faction standing'
2. Underneath this option a menu item for each known faction and their current standing like 'HoA - Neutral'
3. For each known faction player has access to a menu to set the following values:
a. Hostile = Shoot without provocation
b. Neutral = Self defense - Will return fire on any ship but not if it takes damage, only if the enemy is actually targeted them and shooting them (no friendly fire mistaken for hostility).
c. Ignore = Like the current player ship AI

d. Protect = Will intervene to protect members of this faction
So one might set in the campaign:
Plutarch = Hostile
Heart of Albion = Protect
Republic of Cantera = Protect
Everyone else keep default (Neutral).
If one didn't want to risk losing any more faction with plutarch because they plan to make nice later then they might choose 'Neutral or ignore.'
This would be similar to the 2 state friend or foe of X3 only it really needs to have 4 states so that the player asset AI knows how to resolve more complex scenarios that might incur faction hits whether it not it should risk a faction hit to protect the property. There were cases in X3 where my traders would respond to hostile Argons that would irritate me since I was triyng to build Argon rep as a Terran. I would have set these to ignore if I had the option.
My suggestion would be that this mod should not implement any AI changes itself so that it reduces possible conflict with other mods, rather it should be an optional "base" mod for developers to add improved responses based on player preferences to their own scripts.
Unfortunately I don't have time right now or I might endeavor to learn modding to create such a mod. But it probably wouldn't be too hard for a vet modder as it would just a bunch of variables and a menu system to set those variables.