Removing the /2, /3, /4, etc links for each reply within a topic URL

I’m not sure, but doing noindex on those might be harmful. Discourse is already handling it correctly by using canonical URLs.

If you noindex them, there is a chance that it will noindex the entire page (because they are all the same canonical URL), which would be disastrous. I don’t know for sure what will happen, but I’d be extremely careful, because Google often handles edge cases unpredictably, and how they handle them can change with the updates. I’ve seen weird things happen with canonical tags.

It’s unknown exactly how the ranking algorithm works, and it changes over time, but one other thing to consider is that rankings are a results of inbound links. If an external site links to a /number URL, and that URL returns noindex header, it’s conceivable that Google might not transfer the inbound “link juice” to the canonical URL, which could be detrimental to the search rankings of Discourse sites.

I think it would be much safer to contact someone at Google Search and let them know that the canonical tag isn’t working for a widely-used CMS than try to come up with a workaround that might not be handled in the same way as Google makes more updates.