I might be missing something from the post (which I skimmed), but when the author states that "there’s no way to get only the matched comment back" in the "When Nested Documents Become a Problem" section, isn't that exactly what the $elemMatch operator was designed for?

http://www.mongodb.org/display/DOCS/Advanced+Queries#Advance...

The syntax is a bit wonky, but I believe it does exactly what the author says is impossible.