The logical solution isn't to ignore or remove the karma system, but to use it better.

For example, with sufficient data to analyse, it shouldn't be tremendously difficult to find relationships between users who tend to agree or disagree, and provide each user with a customised view, taking these preferences into account.

(Of course, slashdot took a slant at making it cleverer - by allowing upvoting for different reasons - e.g. funny vs. insightful.)

The greying out of downvoted comments seems to me to be a separate issue to karma - and particularly egregious given that (thanks to pg) there are no standards at all for voting.

It would be nice if HN would allow sorting of threads by various filters, such as time of last reply, and/or decide whether or not low-sorted comments get greyed out.

With your suggestion, you wouldn't be able to see the content at all. It would have been deleted.

But I'm very glad they grey out comments, including some of your own. So what do we do now ?

Rarely happens here, in my experience. Significantly downvoted content almost always has severe issues, either in form, tone, or quality. We sometimes might happen to agree with some controversial opinion that has been downvoted a good bit, but more often than not the tone was just not conducive to a good discussion. There's probably a few exceptions I guess, but overall the false positive rate is low enough for me.