I also read that story this weekend.
I think the lack of internal reference for scale etc. could be indeed problematic using spheres but I just couldn't lose the impression that a lot of the story and the problems mentioned were...over-rated so to say.
I also saw the movie in the theater (unfortunately) and I've seen way better CG sequences.
Let's say I wasn't really impressed at all, and believe me there's no way I could ever do what these guys do or even get close to it, but I think much of the discussion in the article is quite exaggerated.
Though I must say that the sequences of Gort "digesting" stadiums, trucks etc. looked quite awesome.
But the spheres, no.