I've taken a look at how other platforms handle muting and blocks/mutes are generally just applied to your own posts (well, also prevents mentions/DMs). I can block someone on Twitter and they can't respond to me but I can still see their comments elsewhere (as well as view their feed). This also happens to be more efficient for the backend. For the sake of simplicity and efficiency, my preference would be for a user's mutes to be applied only to the discussion threads a user starts, and no longer across the site. This gives the author more control over what kind of discussion they want to highlight, at the cost of having to see comments by the same user on other parts of the site. IMO it would be a net gain.

As for using comments to discuss reward disagreement, it's convenient but not a guaranteed ability. There's a disable_comments option in comment_options which doesn't allow anyone to comment. I don't agree this was a good idea, but it's one way ability to comment on a specific thread is already not a guarantee.

It's hard to have any control over basic ordering in your own discussions as a normal-staked user. You can try to flag junk but there are a lot of users who can override your preferences by force, and this is often done not to bring light to valid criticisms, but rather to "mess" with the author.

On this continuum is also the option to whitelist certain accounts, like community-supported bots fighting plagiarism. Listing the muted comment authors in order of highest SP to lowest would be an interesting way to display the most interesting mutes first. Users would see patterns and if they were engaged in the site long enough I'm sure they would explore the muted side of discussions.

A large proportion of users come to the site just one time. Regardless, the impression anyone gets from the discussion may determine if they see any value in engaging further. An unordered mix of spam and harassment among the discussion may likely increase the echo chamber effect. It's just not welcoming.