Here's the thing. If one is going to lose karma for taking (or picking up) something that is not theirs, then ALL actions including looting a corpse and even scavenging (like picking up stuff found in an empty town) should give bad Karma. Nothing is owned by the character unless the character earns it, buys it, or receives it as a gift. Therefore, the system is flawed. Either remove karma all together, or make it a more strict.
A second question to ask, is
if karma were to be changed to be more strict, how should it affect the game? My belief (because in real life, I don't believe in Karma), is that it would be more like what Luck does in the game. It's all based on chance.
On the flip side, I would suggest removing Karma all together. I would not say that "stealing" is always bad. Think about it in terms of taxes. The government is taking my money and using it for things I don't agree with. That's stealing in my mind. Yet, if I were to withhold some of that money, I would go to jail. This is the same thing as what Robin Hood did, and what the King did to the poor. He imposed higher and unjustified taxes. In the fallout world, the player is in a time of survival and war. Is fighting a war wrong or evil? Is defending yourself or preventing an enemy from attacking wrong or evil?
I strongly believe that karma should be removed, and factions should take over.