You could argue that these are not actually fungible products, that when buying from the independent store you are also paying for a public good - the existence of independent stores.
The book is the same where ever you buy it. You could buy the book at Amazon's price and donate the difference to the indie bookstore and the indie store would likely make more from that donation than from you having it bought from their store, and you'd still get Amazon's free shipping.
Small businesses are generally not set up to accept donations, and it may be significant that the publisher records the sale as having gone through independent channels vs. Amazon.
Message board theorizing aside, the best way to support independent businesses is to do business with them.
For a business to succeed it has to provide value commensurate with the price it charges. If you can buy the books at independent bookstores at substantially lower prices elsewhere and you buy them at the indie anyways solely for the purpose of supporting them then that isn't doing business, that's charity.
If your business is actually a charity, consider going non-profit. Non-profit places to get books already exist though, they're called libraries. Independent bookstores sell the same books for more than Amazon so they can't compete as a business and they cannot compete with the state sponsored information access the local library system provides.
All that's left is to open up an overpriced coffee bar and serve the hipsters who find the irony of the bookstore's continued existence appealing enough to walk in the door. It's already amazing such stores survived Barnes & Nobles rise during the 90's and early 00's.
We could perhaps say the actual experience of shopping is not fungible. Normally, you'd find this person simply go to the indie store rather than showroom whatever multinational. Price here is secondary.