Can Drupal built-in search or Apache Solr find comments on the site made with Disqus?
Looks like it may be possible on the server side via the Disqus API PHP wrapper - I widened my answer outside of Drupal to get more input: https://webmasters.stackexchange.com/a/52159/3738

Though I still have concerns about not fully controlling the comment data and if the API changes. I'd have to see real benefits for our situation for Disqus to be able to outweigh these potential issues. Another issue is that of usability (UX/User Experience): having already logged in to the Drupal site, the user has to log in yet again to use disqus, unless the well supported Facebook login to the Drupal site can be "carried" into the Disqus login automatically. Though some user testing has revealed some would prefer the Disqus approach to be simpler.