"Individual stores are responsible for, respond to and correct the vast majority of issues. If you have a concern with a product or service, please contact a Shift Leader at the store where the problem arose."
From their website. So I bet the anti-gun thing is on a store by store basis, and the general manager is the one who has the power to choose whether or not they allow guns. But I bet if we can find the e-mail or phone number for the company owner, then he might be able to talk to the manager and fix the problem.
http://www.wholefoodsmarket.com/customer-service
I'm still looking, I'll let you know if I find it.
All I seem to be able to find is the number for their world headquarters. Might be able to somehow get transferred to John, or have someone give you his e-mail so you can send your letter directly to him. Don't know if it'll be of any help, but it doesn't hurt to ask.
512-477-4455
512-477-5566 voicemail
512-482-7000 fax
And apparently this is their customer service number for their main office. 512-542-0878
Kind of interesting to think I'm only like 20 minutes from their world headquarters.