Seeing as how he is being civil in the manner, as a business I would refund him, as a individual person, probably not. He has a definite interest in "BB guns" so airsoft may not that far off. So he is a potential long time customer as well. Instead of modify the package, would it cheaper to slap a more noticeable "6MM" sticker on the packages? Then using that to update your website pictures?
You could also try a disclaimer at then end of the confirmation stating the sizing of the bb's.
I have no idea what it goes in producing the packaging for your product, but I gather then less money you spend revamping, the more you will have in your pocket, guaranteeing my present and future purchase of BB's
Just briefly browsing your website, I notice you do state : "Dimensions: Round, 6mm, for Airsoft 6mm Gun use Only." I think putting that in bold/underlined would go a long way.