I guess that it's not great to have such a request come in, but if the customer hasn't used the service at all for months, what would you actually lose by giving them a refund?
But if they genuinely didn't use any resources, depending on the payment processor, card charge fees are not refunded - Stripe does this.
The chargeback has happened because the customer isn't satisfied with the refund policy.
If the company had pre-emptively issued a refund (perhaps minus a small admin fee to cover the transaction costs), then the chargeback may have been avoided entirely. The customer may have been happy to receive $3000 back.
I would have a lot more sympathy for the company if they could quantify specific costs they have incurred in providing the service.