Sorry to bump, but after talking with FNW and KLS last night about this, the newest build has a solution:
KLS: Added a field that allows you to override a factions innate desire to assist their own faction in battle to the npc_faction table
Required SQL:
alter table npc_faction add column ignore_primary_assist tinyint(3) not null default 0;
Setting ignore_primary_assist to 1 will prevent NPCs from assisting their own on that faction, leaving at the default 0 will leave things as is
