The very fact that one has to ask if natural, quality backlinks could be hurting a site demonstrates just how confused SEO has become since Panda and Penguin. :/
It *shouldn't* hurt you, but am I right in understanding you're still looking for an explanation why Penguin hit you? If so, Penguin is not just about backlinks. There were sites hit with clean backlink profiles, so Penguin has to be looking at other factors it considers spam. Unfortunately, I can't begin to guess what that might be for you - I'm still not sure what it was on my site.