I think the solution can actually be dedicated Q&A forums. For general discussion it can get quite messy. If you have dedicated Q&A forums where the replies are actually answers to the question (not discussion) and they can be voted up and down based on the quality of the answer (and physically move), then, comments could be open for the replies, as in: "This answer sucks!" "This is not true." "You are wrong," etc. Or: "I agree with this answer, but I would like to add..." (blah blah blah). For it to work you would have to make sure a reply is an official answer, either with a disclaimer, or by restricting the poster to one post only, or similar. Comments would be unlimited. Think Yahoo! Answers.
THEN to me comments work.
Keep discussions separate, add Q&A. Would love that.