Great question — answering as the UphillTech team:
You should re-read: http://www.nichepursuits.com/how-to-get-a-google-penalty-using-affiliate-links-and-how-to-recover I should also point out that all of these links were “cloaked” affiliate links Generally affiliate links do not harm SEO unless they are coming from a harmful network... The biggest reason many sites get slapped with a penalty is because they try and hide (Cloak) the links from either the search engines or its visitors with one method or many.. Which of course is against their policy. Google can't punish genuine affiliate networks as they would soon find themselves with endless court cases with Google pushing affiliates out of market place and arguable would be because it...
Full answer by Simon Hayter: https://webmasters.stackexchange.com/a/52652 (CC BY-SA 3.0).
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