[From Lucas' answer]
About accepting a 'comment' that is in an answer box. It has more to do with the interface, in my opinion. Anyone coming from any other place, (intuitively) you see a chat box, you write there (like most forums), but to actually comment, you have to hit "Comment on this Answer".
Possibly change the 'Answer' text box, to "Answer this question" button, then open the text box or something like that. Which might alleviate the answering a comment thing.
[Image Analyst's suggestion]
Maybe you'd want it to recognize that the person submitting an answer is actually the original questionner and to ask them if they really want to answer and accept their own question or comment on another person's answer? That might not be a bad idea.