I'll bet Google makes a mint out of affiliates on Adwords AND Adsense so IMO they're going to try and find the balance between providing value to the searcher and their revenue streams. IMO an affiliate will continue to prosper under Google if they provide value-added content.
Example: brands often don't supply a good cross-section of honest product reviews (or they prioritise the better ones!) while an affilite can be more up-front. That can add real value for a user and it makes sense for Google to use it. Which, TripAdvisor, Sidestep etc...all virtually indispensable affiliate sites.