Do we know he deals with chaos? As far as I remember, we don't. We saw him be radical back on 31-12, were he got into contact with that black sludge stuff. But we don't know if it had any affiliation with chaos whatsoever. In fact, we saw Cultists, and we can guess that there were some Nurgle-Daemons aswell, but they got killed by either our plasma warheads, or whatever it is that causes the rain to be that toxic and lethal. =I= would have told us if it was of chaotic origin, but he didn't, most likely meaning it is something best kept unknown to the normal guy.
They do this all the time, and the only people having a general knowledge of all the enemies of the imperium are commisars and the Inquisition. The fact that he was trying to get rid of us, if just for a few hours/day, however long we actually travelled through the black hold, tells us one thing, which we knew beforehand: He's an Inquisitor. They do this stuff all the time, and noone really cares much since they are beyond the chain of command. Something sinister is going on down there and the only one who knows what it is we're fighting, is the one guy you wanna shoot because he MIGHT be tainted, and that after we just walked out of a black hold alive, with 6 mutant friends, yet you expect to live through all of this after shooting him, because we can tell on him. Doesn't really sound coherent to me.