I believe you meant to say "it proves your business isn't as squeaky clean as you make out". With a response like that, clearly their business was operating in some kind of grey area. It's unfortunate that when this happens, the company (ex: Stripe) can't come back and disclose specific details about the scumbag making a stink on HackerNews over something that the company was perfectly in the right to shut down.

Unfortunately, a lot of businesses want to accept credit cards online with little to no effort in managing the risk. 1-2% doesn't sound like enough wiggle room, but if a company isn't using misleading marketing, is not defrauding users, has a product actually worth what they are charging, and offers instant support for refunds - then staying under 2% is not difficult. Too many businesses want the risk to be handled by external forces. If you want to accept money online, make sure your business is prepared to manage the risks. You can't just drop in the payment processing and wait for the money to roll in.