you would need to use the api to track conversation flow from the original tweet down through the replies, I tried to do something similar at work for our blog but the problem is not everyone (mainly 3rd party tools) don't reference the original tweet when sending the reply and just @mention the person instead, which loses the link to the original tweet.

maybe adding the ability to comment using twitter auth rather than entering an email address would entice people to comment rather than tweet?

I agree a comment on the post is much more helpful than a tweet reply, not just to the author but people reading the post further down the line, I have a couple of posts where comments have helped people reading it 12+ months later. If they were sent as a tweet instead they would have been lost months ago.