Your point is reasonable enough. I am not familiar with these books, but if the consensus was that $55.00 compensation for this issue was a significantly inflated (and therefore abusive) price for the book, it would be more understandable if the seller balked. Nobody wants to feel like they are being put over a barrel.
That said, when I see a $25 dollar difference, which presumably could have been settled for less drama at an earlier time, I remember that old (outdated?) saying "the customer is always right". Of course it doesn't literally mean the customer is always right, as a customer can be abusive or unreasonable, but its a philosophy that puts effort into customer satisfaction, and that often helps avoid getting into these situations in the first place.
If you make a mistake, and you know you've made a mistake, fix it quickly and make it right, and 99% of customers will go away still happy.
I know nothing of the rarity of the book in question etc, but if I buy a set and its missing 1 issue from the set and the only way for me to complete the set is to buy it from ebay seems like an obvious solution.