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Ok another tricky situation. First of all, I would like to ask you to create a Google Webmaster Account with a new Gmail id for this Domain.org [since you are worried about the association, though I can assure you there is no such thing as association with a penalize website will incur penalty for other websites ]. _So, you need to create a Google Webmaster Tools account to figure out whether the website has got penalized by Penguin update. If you have received any message in Google Webmaster Tools account regarding link warning, you need to get all the spammy links removed before applying for a reconsideration request. However, if this is an algorithmic penalty, you need to give a try to Disavow Link option. _