I suppose karma spread by teaming hasn't been taken out yet? This is a good example of why it shouldn't be in the game. It really really is an annoying mechanic.
At the very least, it should only affect your karma if you team up with someone of the opposite extreme alignment. If you team up with a nuetral character, in my opinion, it shouldn't change your karma. Or teaming could just not change your karma at all.
Furthermore, I would like to say karma only seems to be a measurement of how many undead you kill and people you team up with, and perhaps beggars you give money to. It doesn't feel like if you are trying for good karma, it doesn't measure how good of a person you are, just those very specific things. Bad karma, on the other hand, has a lot of support.
Just my opinion.