One thought to consider: this tool warns you not to use it unless you're sure you have spammy links you can't control, and that those links are giving you Google trouble. Who could possibly know this but an SEO?
So use of this tool will out you as an SEO to Google. Some have suggested that's really the whole point of Penguin - to get SEOs to show their hand by trying to fix the problems from an anti-SEO algo.
Just a thought. This is something I've wondered about ever since no-follow - once Google started issuing tools that only SEOs would know about, they had a way to compile a list of who's an SEO... just in case they ever decided to, you know, annihilate SEO entirely.