Here's a perspective from Dr. Bonner's, which makes it seem all hunky-dory:
Dr. Bronner's Response to Criticism of Fair Trade Organic Olive Oil from Palestine
Her objection seems to be that Whole Foods promotes Canaan Fair Trade, which in turn funds scholarships to Palestinian universities that are wont to have pro-terror celebrations.
The article also said that Whole Food was sponsoring an anti-Israel radio station
“After repeated requests by many, Whole Foods refuses to drop its sponsorship and donations to this programming, despite the fact that rival Trader Joe has ceased its relationship. Some of “Radio Intifada’s” and KPFK’s fundraising materials specifically attack Jews. But that didn’t stop Whole Foods from donating to them. Learn more about this at Join The Boycott (scroll down).”