If a Rogue trader became aware of one of the dodgier factions such as the Istvaanians what could he actually do about it?

Secretly assassinating them seems about the most straightforward if you can pull it off without leaving anything traceable back to you...

Taking up with one of their rivals in the Inquisition seems like another approach (which could be ironic if the one they ally with is actually from an even more evil faction).

Any other idea's? It's not really a profitable thing but potentially something a loyalist Rogue Trader might do.

If you take the default setting of the Koronus Expanse, the closest ruling Imperial body is the Calixis Sector, which is basically openly governed by the Inquisition. Everyone (at least thinks that they) knows where they are, who's in charge, and the rough division of three major Ordos. As a result the answer to this is a political problem that a Rogue Trader is theoretically able to solve.

Control who is sent in to investigate this.

Get a sympathetic or loyalist Inquisitor, or one that you have worked with in the past or you know hates Chaos and can make your case to - ideally BEFORE the assassination - and things can go really smoothly for you.