It should be clear that I don't think debate is the only way to refine human rationality (or I wouldn't have posted a piece of fiction), but I can't think of anything that can replace the essential function that debate serves, in clarifying people's positions and arguments, getting them to reassess in light of new information, and possibly reaching a consensus that updates on all relevant information. We're certainly not at a point where we already know what rationality is, and the only remaining task is for everyone to learn how to practice it.

I agree with you that online debates can easily become distorted due to the nature of the medium, and I think we should try to find ways to reduce that effect. I submit that one of these distorting effects is how easy it is to ignore a contrary argument. (I think it's probably even easier to ignore contrary arguments in academia, and we should try to fix that as well, although that's a much more difficult job.)

If the commenters want to have a debate and that isn't what the original author wanted, all they have to do is write a new top-level post.

I still don't like this idea (of having the author moderate the discussion), but others might, and it seems largely independent of my suggestion of a disagreement status indicator. You should probably propose this in a more prominent place and get other people's feedback.