Although it was shot on 35mm film in a 1:1.37 format it was always intended for cinema exhibition in a 1:1.85 format. A lot of films are shot in this way and later matted into widescreen (including the first two Harry Potter films but I don't think anyone would suggest they were intended to be shown in full screen)
If you look here there is quite a lot of discussion on the subject including some input from Joe Beirne the Producer of Naqoyqatsi, and the premiere of Koyaanisqatsi was presented in widescreen as intended by the director.
Again this is very cool and thanks for seeding, I do like to see open matte versions of films just for comparisons sake.