As far as stealing from powder gangers go I understand, your not stealing from powder gangers, your stealing from whoever they stole the stuff from.
I can see where you're coming from, but I think it's just a mistake in coding. If you want to open that pandoras box of ownership chains, almost nothing in this game would be safe to take because everything has belonged to someone else at some point. Besides that, what makes anyone think that the person those goods were stolen from is still alive? Are we to think that it is better to just leave it out to the elements or leave it for other criminal elements to retrieve and use against more innocent people? We could even make the case that taking from the powdergangers should give positive karma, not negative. No, I don't think there is any complex thinking behind this, just an oversight that's needs to be corrected.
Anyway, if the powdergangers issue was deliberate, than it is highly inconsistent with the Vipers, Fiends and other criminal elements who outfit themselves with raided goods, but don't incur karma penalties for looting them.