Nope, there's no penalty for using your favorite weapon!<br/><br/>Just for having things happen to you that please the chaos gods.  It's really not going to happen THAT often, and don't let Glyphsone give you the impression that it will.<br/><br/>A genre assumption of Rogue Trader is that the PCs are people who the Chaos Gods really want to turn into their servants, and corruption represents the attempts of the Chaos Gods to reach out to the PCs.  When you gain corruption points, you move closer to service of the ruinous powers, though it'll ultimately be your choice if you sacrifice your body to chaos to save your soul, or sacrifice your soul for power...<br/><br/>In other words, it's a plot thing, not a gameplay thing.  you didn't get a corruption point for using a bolter, you got a corruption point for pleasing Khorne.  He'll be harder to please next time!