@Lithium Not to mention the -vast- power disparity between Inquisitorial Acolytes, Imperial Guard, Rogue Traders and Space Marines. So first thing would be to pick which game to focus on I suppose.
It is late so my brain is a little fried so take this with a grain of salt but obvious first step would be to pick which game to focus on. I just had a thought that Deathwatch might work best, as teams may shift about based on the needs of the mission. Of course not too much to do in downtime, although the RPG game does present them as more than biological robots.
Could have a rogue trader flotilla, with folks as fairly junior crew members. Basically something with a hierarchy that -really- frowns upon killing off other allies.
So Dark Heresy is probably not your best bet, as killing the acolytes of other inquisitors is not that uncommon.
Just some thoughts, sadly I don't have a great solution for you.