Hmmm. My unease with this idea would be entirely resolved if the upvotes were cached until the user reached 1000 karma rather than merely prohibited/lost.
Consider EYs article on how we fail to co-operate; I'd like to be able to stand-up and say "yes, more of this please". I don't mind at all if the effect of that upvoting is delayed but if I reach 1000 karma I don't expect to find the energy to go back over all the old threads to up vote those I liked in the past - so in that world my expression of support will be forever missing.
That said, something really is necessary - on more recent posts the comments have had such a disheartening effect that I was beginning to decide that I should only read articles.
The thing is your early up votes and down votes are probably different than your later ones.
The recent implementation of a -5 karma penalty for replying to comments that are at -3 or below has clearly met with some disagreement and controversy. See http://lesswrong.com/r/discussion/lw/eb9/meta_karma_for_last_30_days/7aon . However, at the same time, it seems that Eliezer's observation that trolling and related problems have over time gotten worse here may be correct. It may be that this an inevitable consequence of growth, but it may be that it can be handled or reduced with some solution or set of solutions. I'm starting this discussion thread for people to propose possible solutions. To minimize anchoring bias and related problems, I'm not going to include my ideas in this header but in a comment below. People should think about the problem before reading proposed solutions (again to minimize anchoring issues).