It's not the personality thats the problem, it's that if it has a green ticker, some of us like to talk to it, it's completely possible to hate a faction but be willing to talk to it. It's cool they'll have a detailed history, but to use your words, they become 'automated drones' as soon as they see their hated faction, which is ridiculous.
*nod* But my problem with it is it being "either way automatically"- I can see the over-the-top problem with
all followers, for example, having a hated faction that they attack any member of on sight. But on the other side of the coin, I can also see it being sensible (given an appropriate background) for some normally-calm followers to hate a given faction, but be able to control themselves- until they see that
one member of that faction who sets them off. Random examples being "That's the one who [killed my brother/sister/loved one, ordered my hometown razed, etc.]"
And to clarify, while I see what you're saying, there's a reason I said "automated drones
slaved to the PC."
But to really put the RP into RPG, why not have followers with hated factions/persons have some dialogue at some point where, depending on certain factors, you can:
Find out what person/faction they carry this blazing "kill on sight" hatred for
With speech checks or appropriate dialogue path, convince them "We'll get them, don't worry- but don't open up immediately, we can get something from them
and get your vengeance."
Bottom line being, let'em have their own motivations, and work it into the story.