Personally, I think it would be hard to deal with these kind of issues just as Iwata states. The issue you pointed out, where nintendo shut down a fan-made film based on the Legend of Zelda might have been necessary.
If the film were going to start actually turning a profit for the creator then they kind of crossed the line where they're profiting off someone else's intellectual property.
I wonder about this all the time. I log into Gmail with an encrypted connection (https). So if I send personal email from here, I'd hope that its off limits and they can't see it, but on the other hand... is it really?
If IT take a screen capture or grabs some key strokes from a personal email, I guess its technically not off limits.