Unless I'm misreading the article, I don't think it says that Thor: The Dark World was a prequel to The Avengers. Rather, it says that the Thor movies were planned as part of the "Avengers initiative." The confusion arises from the phrase "set the stage for The Avengers." I think what the writer means is that all of these movies, including their sequels, were set into development as part of a single initiative, meant to culminate in the Avengers franchise.

Yes, the events of the second Thor movie take place after the events of The Avengers. But that may have been planned well in advance.