A conversation with 2 to 6 participants (EDIT: about a controversial topic) can be pleasant, can be thoughtful. The same conversation with more than 20 engaged participants is always awful. Here is my solution to solve this inherent problem of comment sections with many users.
This approach is only intended for comment sections of articles on politics. Its not supposed to work for a Q&A community. Sorry Edie
Let us view the top-level comment as an opening to a debate. The author of this comment is going to be one participant of the debate. One of only two. Its is going to be a 1:1 discussion.
After the top-level comment has been written, every other user is allowed to write an answer (not more than one per user). All the answers are displayed indented below the toplevel comment. But nobody except the author is allowed to answer on the answers. Got it? You can view an answer as a proposal to a debate.
Once the author of the top-level comment has answered to one of the proposals, the 1:1 debate starts: The participants are the author of the top-level comment and the author of the proposal that has been answered by the author of the top-level comment. Nobody else is allowed to take part. Since it is an 1:1 debate, no more indenting is necessary. The debate is easy to follow for the readers of the comment section.
All the other proposals are collapsed to the single sentence: "(+) show more answers to the top comment".
I think Courtney would love this approach, because her well articulated comments would finally pay off.
Maybe you think that is approach is to strict. And there should be a possibility for other discussants to join the conversation.
So instead of just prohibit other users from answering to an answer of such a conversation, lets use the "reply as a linked topic"-pattern from Discourse(TM). So other users cannot join the conversation, but they can create another top-level comment by using the additional interaction ~"reply as linked topic". Using this method the author of a top-level comment is able to debate with more than just one of the answering users. But in completely different threads.