This idea is credited to my girlfriend, which is why I post it now even though its probably a little late in the development.
The idea came from me explaining that in regards to moral-compass the Inquisition has two "main" groups. The puritans; if in doubt add more exterminatus, and the Radicals; brothers with this demonblade I could save humanity.
Since it seems that atleast the choices between the different faction will collide at one point, she suggested that it would be cool to have a hatred-system which could reflect the times the other faction had gotten the better of you in some manner. (Since I am unsure how conflict between faction/cabals are gonna play out it also hard to specify how one would benefit from such a system.)
She suggested that if the faction of the playerbase becomes heavy on Puritan or Radical, the minor could get a SLIGHT increase in cabal exp, difficulty-rating on missions or in the extreme 1) bonus in pvp and/or 2) additional options in priority missions.
This is just a rough outline of an idea, but when she mentioned the idea of using hatred as a stat/or whatever I was totally sold on just the sheer "Warhammer 40k vibe" of it.
Sincerly, from the better half of,
Vlricus von Kronstadt