Should the author have the privelage of moderating their comments? They could shave off all the comments that threaten the authors argument. Suddenly its become a single sided debate.
Authors can moderate what appears on the same web page (their own site's comments, if any) but not what appears in other places (Twitter, Reddit, Hacker News, and so on).
Putting comments from a different community on the same page as the original article is a mashup of sorts; you're mixing content from different places. This can create confusion.
It seems like if such mashups exist, they should have their own URL? Suppose that when following a link from Hacker News, you get a web page with Hacker News annotations.
What URL should that be? Maybe it should go on ycombinator.com, sort of like when you embed a YouTube video.
Therefore the moderation will not have anything to do with the content owner. It's comparable to reddit or HN : would you complain that content owner have no control over discussion about their content on those sites ?