Comment_karma is a remnant. Much like post_category and link_category used to be. The only difference is that, until recently, there was no way to really get rid of it.

However, now that we have comment meta system, I expect that the comment_karma field will go away. Probably not in 3.0 since we're close to feature freeze. But probably in 3.1. It'll likely be replaced by a comment meta of "karma" or similar. Plugins should start taking advantage of the comment meta now, as many of the comment fields are not really necessary any more and probably won't live long.