I see it as what it is. A book of words. To be sure, those words were meant to subvert an entire culture of people to the whims of a madman, but just a book nonetheless.
Its only symbolism comes from within the one viewing it. I have no reason to desecrate it because it means nothing to me. Those who believe its hatred and lies will do so whether I take out my frustrations on a pile of paper or not.
You say we got to wonder if it is a bad thing to desecrate it. In my opinion, no. But neither is it a good thing. Your viewpoint may be totally different, but that is due to your internal response to the act. It is you, not the book, that gives power to its symbolism.
I'd desecrate a copy of the communist manifesto with less gusto than the koran.