I like the idea in principle, but how would you implement this? Would each comment also have a rating next to it?

That's how I imagined it, yes.

From a developer's standpoint, making a comment moderation system a near duplicate of the idea moderation system allows code reuse and helps keep the codebase clean.

The biggest difference would be anonymity...a lot of the comments are controversial. I'd be much more comfortable giving an anonymous thumbs-up or thumbs-down than I would be posting a specific rebuttal.

Rebuttals to some comments could lead to behaviors like idea-stalking and aggressive downrating of all of one's ideas by an angry and offended individual. That would undermine what I perceive to be the purpose of thise site.

It might further complicate the code but it would be nice if people when submitting ideas could check a box saying "Allow Anonymous Comments" or not. You might realize you'll get more feedback by permitting anonymous entries, but on certain things you might want to know who made what comments. Would be nice if the author had the option.