I was making generalizations based on the fact that it was not shot in 3D, and that would lead me to believe Whedon didn't want it in 3D, but had no say in the matter. Post-converting makes no sense if the director knew all along he wanted it to be in 3D.
This quote right here,
from this article makes it sound like Whedon pretty much had no option in whether the movie would be in 3D or not, and it doesn't sound like he intended for the movie to be that way. "The writer/director added that he supported the idea to release the film in 3D. "Yeah, it's fun!...I'm not a big fan of extreme long lens, talky movies - I like to see the space I'm in and relate to it, so 3D kinda fits my aesthetic anyway. And the technology has advanced so far in the past couple years."