Comments are great for annotating questions and answers but are lousy for dialog between users to pin down clarifications that may ultimately be reflected in the question or answer itself. Unfortunately comments are currently the best that there is so far, so until a new feature is added there is going to be an unmaintainable build-up of comment cruft, including comments that are made irrelevant by later edits to questions and answers.
There have already been feature requests here on meta for things like threading comments, notifying comment authors about comment deletions as well as automatic comment deletions. I understand why these have been rejected. The fact of the matter is that discussions-via-comments often lead to improved question and answer quality but I think that there needs to be a way of removing discussions and references to outdated versions of Q&As after the question and answer has been improved upon clarifying what the author was trying to convey.
As an example of what I mean, have a look at question 4928930 where an ill-posed question was salvaged by a dialog that forced the asker to have a good look at his code but now all these irrelevant comments everywhere remain.