Link's the hero in the classic sense. He's not Batman where there's a skewed sense of justice, he fights to save the world and his loved ones.
And in The Wind Waker, lines were pretty blurred at the end of it, but it wasn't because Link got his hands dirty to get the job done (it was due to the NPCs

).
I think I get what you're saying. Ocarina of Time was a classic story of good vs. evil. This one looks like it'll be more of the same because of its strong resemblance to OoT. Though, looking at Majora's Mask, and The Wind Waker, I think Twilight Princess will be even more advanced in its story telling. I think Aonuma and crew really know what they're doing in that department.