Eugine admitted his guilt,

Did he admit his guilt, or his actions? From the outside, it sounds like the latter.

Although the wording does not explicitly mention downvoting, harassment by downvoting is still harassment.

Begging the question that mass downvoting amounts to harassment. Downvoting is downvoting. Votes can be positive or negative. Would he be similarly banned if he had karma bombed positive votes and it made people feel all warm and fuzzy?

Needless to say, it is not the place of individual users to unilaterally decide that someone else should be "weeded" out of the community.

I assumed it was everyone's place to decide how to cast their votes. Think globally, act locally, yada yada. Ironically, he was acting in accordance with the widely held view that some people needed to be silenced to improve the atmosphere.

Several users have indicated that they have experienced considerable emotional anguish from the harassment

People told you he "made" them feel bad. I guess "Feel Bad" negative karma votes are ok. And get a lot of action from those with power too.

The fact that Eugine remained quiet about his guilt

He remained silent about how he voted, in line with the privacy configuration for votes, which has now been explicitly violated by those with the power entrusted to them. Bad precedent.

is indicative of him realizing that he was breaking prevailing social norms.

Really? Breaking social norms is now verboten in our community of polyamorous transhumans?

Seems to me he was simply acting in accordance with one prevailing norm (one that I disagree with), by violating another (that I agree with).

Eugine's actions have worsened the atmosphere of this site

Other people were part of the causal chain of a "worsened atmosphere". Assigning him as "the cause" is a judgment. Me, I'm not enthusiastic with the prevailing culture of "I'm upset, therefore you're wrong."

I asked the community for guidance on dealing with the issue.

And the pitchforks came out. Three years, 9000+ karma. Now, banned for life. The mob is fickle.

Funny thing is, I was equally unimpressed with all the signal to noise complaints. I've turned off filtering based on karma. I'd rather filter based on vote count than vote sum.

I find an atmosphere of bad feelings and social shunning rather tiresome all the way around. Buck up and don't shun - that's my preferred atmosphere, and that goes for Eugine and the concerns about signal to noise as much as those who would ban him now for hurt feelings.

All indications are his negative votes were for people being MoreWrong, in his opinion. Having people think you're MoreWrong is unpleasant. I don't think the ideal answer is to shut up those who share that opinion with you.