Stripe has the ability to negotiate with their upstream processors that we end users do not. Instead of trying to reduce their costs by pressuring their providers, they're passing along the fees to their customers.
If they're intent on working with the customer to keep prices down, they should only charge a fixed fee for refunds (to pay for overheads), and not the interchange fee.
[1] https://news.ycombinator.com/item?id=22371571