I also tend to play down chaos/aliens in games that I GM, mainly because I think that inquisition (or other imperial body) vs. chaos/aliens is a very overdone concept.
Most of my campaigns these days revolve around the darkness and brutality of the Imperium, and the sorts of human monsters that it can create. Those of you familiar with the Hive Maiden might remember the character "General Magellan", a monster of a man who, whilst still free of xenos or chaos taint, has become something really quite foul and horrifying. He was an Imperial Guard general whose mental state had deteriorated through decades of war, and every time he butchered a child or murdered a colleague for his own perverse pleasures, the Imperial government covered it up, since he was still a very good military leader.
That sort of coverup/conspiracy is the sort of thing that I normally have players poking around in. It's dark, it's gribbly, and it's a far cry from the cliched: "You are inquisitors. This is a demon/alien. Kill it."
So, in that vein, I applaud you for your very understandable and unique "human" enemy. He's powerful, he's scary, he's a threat to everything that the Imperium holds dear, and he's definitely not cliched.