I guess you'd have to make a separate karma for story submission then.
Isn't the concept of karma what motivates most story submission anyway? Story submitters want Google karma (a.k.a pagerank). I have submitted about half a dozen stories, and that was always my motivation. Taking away some of this incentive for those who abuse the system might help the problem. I think it should be retroactive as well. Once your submission karma is poor enough, the nofollow should be added to all of your past stories.
I see two problems with the scheme. First, it would require adding a layer of complexity to slashcode. Second, it would not solve the problem of people submitting stories about their own blog who merely want ad revenue from page views.
All human relationships depend on trust. Mechanisms for evaluating and developing trust need to change as the scale of the relationship changes. The "Wild West" days of Slashdot story submission may be coming to a close because the huge scale necessitates developing a new mechanism for evaluating and developing trust. We can all shed a tear and have a moment of silence for the innocence of Slashdot's youth, but I think it's time to acknowledge that we have outgrown the old method.
Honesty is for the most part less profitable than dishonesty. -- Plato