The email idea would be great. I've had trouble responding to comments on articles I've written until I learned I could just subscribe to Disqus comments. Ideally the author would publish the email response to the article if appropriate.
And for articles where the author doesn't provide an email address they can be reached at maybe those don't have comment sections as it does now.
Maybe offer an intermediary communication method like an anonymous email address for emails for just that post to go through.