Sure, to us reading from the author's blog, we know it's an independent video. To most people who would load up iTunes and see a big banner for a Steve Jobs video on the front of the store, it would seem as though Apple were behind it.
I don't think there's anything wrong with not actively promoting that sort of confusion.
If they'd really thought it was "too controversial" (Not sure why the author quoted that phrase, and then didn't say if it was an actual quote?), they wouldn't have put it in the store at all. It's not like banning something from their store is something they're afraid to do...