A lot of people are debating this right now. I think the general consensus is that it's working as intended, because you're still taking something that doesn't belong to you. I find it kind of annoying, though, because just about any kind of scavving is going to involve stealing from someone, unless it's a group that's hostile to everyone. On the other hand, I don't think karma has nearly as much of an effect in this game as it did in FO3.
It's especially silly if I blow apart a dead Powder Ganger, loot everything off of his corpse leaving his dead body to rot in the sun in nothing but undershorts, and then take two steps to the left and get a karma hit because I plucked a hammer off a table.
That just can't be working properly.
But I do think that you're right... it looks like reputation is far more important than some of these smaller karma losses, so I've been looting away.