As far as I’ve understood looking at the code, *WordPress* only knows about a comment having been written after Disqus syncs it back to your WordPress instance.
Thus, as far as I can tell, to implement notifying the WordPress post author, you’d have to implement it as some kind of a Disqus plugin on the Disqus infrastructure; based on a quick Google search, that doesn’t seem to be possible as Disqus doesn’t seem to expose a plugin interface on their own infrastructure.
The only option I can see would be having Disqus sync the comments to WordPress but not actually save the sync results in the WP database but only use it to trigger the notification emails. I haven’t looked into this as it would require overriding the functionality of the Disqus WordPress plugin itself. The overriding could hopefully be accomplished without modifying code on the Disqus WordPress plugin but then again it might not.
Would you be interested in looking into the matter and possibly contributing code?