The problem with Disqus is that it uses JavaScript to render comments, so when robots come to your site, they don’t find comments. Even if it uses the index "#!" URLs are still not your page, so they are not applicable here.
They have a REST API that you can use. My idea here is to bring all the API comments by code and write them in HTML inside one container, and then hide that container using JavaScript (not CSS, since I'm not sure if robots will hate this, but JS doesn't detected).
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