I definitely see your point: if the system is automated and objective, (that is, without any component of public shaming), trolls won't feel as much as though it's a social norm preventing them from posting so they will feel like it's OK to work around the system. However, it's the atmosphere of public shaming that makes me uncomfortable.

We could try to emphasize the social norm as much as possible in the About description, something along the lines of, "If you have negative karma, it is because the net opinion of readers on Less Wrong of your comments is negative. Thus, users with negative karma are discouraged from commenting by an interruption in their ability to post comments."

Also, I submit that it wouldn't be that rewarding to sock-puppet yourself to positive karma, just to post a comment and get negative karma again.