I don't feel this is very much an issue with the karma system, just a problem with "mean people suck". No matter what technical system is in place, there will probably be some ways for people to be meanies---sending lots of nasty personal messages from behind a TOR proxy, for instance. The fact that in this case they decided to (ab)use the voting system is incidental, and a solution need not involve making any dramatic changes to how the voting mechanisms work.