This article will seem a lot less threatening if instead of titling it "Google Becomes an Affiliate" they had considered another way they could have phrased it: "Google to start charging a fee for Google Base." This is an opportunity, not a disaster.
See, Base has been around for over a year. Base ads get preferential treatment on Google searches -- in fact, they show up at the top of organic search results, rather than in the ads. However, it's currently all free. This is just letting people pay to get their Base ads above others -- right now, it's all determined by listing quality, low price, and CTR.
What Google is proposing to do here is just turn Base into a Google-integrated shopping.com, Yahoo! Shopping, or Live Search Cashback (or Bing Cashback or whatever the hell they call it now.)
Right now, Base forbids affiliate ads. They do this because Base placement is actually outrageously favorable in search (my most successful IM effort ever involved putting affiliate ads in Base, which got me $36k in under a week before Google not only banned my account but also changed things such that my scheme was no longer possible.) If Base listings become paid, will Google allow affiliate placements in them? Maybe so... and if so, there will be fantastic arbitrage opportunities there.