Yes, that's a problem whenever you redirect or unify ongoing threads. It's a tradeoff. We'd rather have the best stories on the front page. In most cases, comments eventually grow around the new content.
In this case, though, the space elevator content does come from the real article, so these comments are on topic. The original url was basically self-blogspam—full of links back to the long piece.
Wouldn't be possible (worth) to split a converstion and make it a first page post on it's own, if:
-it's not directly related to the thread (hijacking)
-a certain cuantity of upvotes are received,
-and a minimum converstion lenght is reached?
Some times very interesting topics or meaningful comments are lost on moderate or low (to first page standart) interest news.
Not many are actually discussing the real article.