Indeed, the sockpuppetry really hit hard around 2010/2011, and I've yet to see a website handle it very well. Honestly HN is one of the last places I take the actual time to comment on because of it. There are some methods that slashdot uses that I think could also be helpful, but there is no easy fix.

Like you said though, one interesting side-effect is that for the astute reader you can discern what the talking points of the day/week/month are by paying attention to the narrative.