Until Amazon credibly deals with its counterfeit problem, I'm not buying any foodstuffs from them. While it's likely that Whole Foods / AmazonFresh supply chains are currently separate, that's beside the point. If the problem goes unchecked, Amazon may consider expanding the strategy further.
People are paying a premium for organic / fair trade / gluten free / $FAD_OF_THE_DAY groceries, so there is margin for counterfeiters IMO.