I understand you think that is the problem. But, IMO Google is not "penalizing" you for having those links. They are simply devaluing those links (which may appear like a penalty.) and also will cause your rankings to drop.
My site was #1 for the main money term before some third party posted them, so they had no beneficial effect to begin with. If they had simply been discounted it would have made no difference.
If you have a better idea than the rest of us about how Penguin operates, please share it.