In relation to this problem, I propose that a new link, reply, be added added after the time indication on comments which opens the comment box and pre-populates it with the @username of the comment that reply was clicked on, as follows:
It doesn't load the server, doesn't add any hierarchy, and is natural and obvious to new users - a UI win, since it teaches them about the @username feature as it does the work for them.
One of the main benefits to this functionality is that when new users post a question and seasoned users ask follow up comments, the new user is more likely to have the correct @ functionality which will notify the seasoned user that their follow up comments were responded to, and they might be better able to answer the question now.
At the moment a lot of questions get follow up comments to which the OP responds, but there the communication ends because the OP doesn't use the @username notification, and the seasoned user doesn't come back.
Humbly submitted for your consideration.