lets look at dan's previous inquisitor story - the comic one. The older inquis goes of the deep end and is hunted down by his pupil. The pupil seems to die at the end of book 2 - but it's likley book3 he would be alive but highly cyborged. Maybe even goes radical himself to ge revenge.
Now, the big thing with Eisenhorn was he loved Bequin but her untouchable aura would have made him insane - esp as he is even more psychic now.
What happened at the end of Ravenor? Fauke - an untouchable- seemingly has his ability burnt out by long time exposure to an emerging psyker. So, untouchs DO HAVE SOULS. It's just this aura that makes it seem like they don't, like a spiritual vortex.
So, Eisenhorn gets corrupted by Cherubael. He steals Bequin and exposes her to psychic power to wear down her aura so he can live happily ever after.
But the way he does it is super radical so ravenor gets sent after him.
In the process, a greater evil is revealed, they join foorces against it, and Eisenhorn dies to prevent it, possibly sacrificing his eternal soul.