I do have one possible solution, though: for every 50 karma points you earn, say, you get a "free gift" of some sort within the system (because otherwise it would encourage gaming of the system to earn such points). One gift could be a one-use "post this comment anonymously" checkbox that would then disappear. Another would be, to use a fun example, the sort of "mega-upvote" everyone wishes they had around for when something truly deserves it.
EDIT
Part of what's neat about this idea is that support now can cost people something, so they have to really be behind what they support. On the other hand, it would probably establish a oligarchy.
Sure, it can be a "noble sacrifice" and generate some sort of epic story retold throughout the community where user-Gandalf sacrifices their karma in the fight against troll-user-Balrog, and then others step in to "forge ahead without them," but just because a notion is romantic doesn't mean it's Utilitarian (in fact, they're almost opposite by definition.) Although boring, the community as a whole is likely better off if the others could restore Gandalf afterwards, as long as they thought his actions were justified. Since, in a database, there's no difference between taking something away and instantly finding reason to give it back, let me phrase it this way (thank Doctorow for this):
You don't spend whuffie; you just have it. However, if you do something stupid with it, it can be taken away.
I'm not sure if this has been tried on a social news site before, and it sounds stupid on face-value, but, what if, instead of each comment having an individual score that also affects its author's karma, the comment's score (and therefore its page placement) simply _is_ the author's karma? That is, a comment by a user with 3000 karma starts off with a score of 3000, and is placed on the page accordingly.
As such, you wouldn't really be voting on the comment itself anymore, but rather voting on the user by considering the comment as an action by that user. Taking all your points off of a user for one especially bad thing they did--considered on sites like this and reddit to be quite uncouth--wouldn't be a "sin" any longer, because _you're not rating their comments_ any more; you're just rating _them_. When you give someone one downvote, it applies across the "scores" of all their other posts, and likewise for upvotes.
I'd love to see this system tried out. I don't even have a special attachment to its success or failure; it simply sounds like a great experiment in virtual sociology. I might even be motivated to implement it myself if anyone else shows interest here in being part of the resulting community.