While GitHub makes millions per year, it's important to keep in mind that "GitHub" and every other company is really just a collection of people like you and me. I'm sure their engineers are paid well, but money isn't everything, and it's nice (and motivating) to show up at the office and know there's people out there who appreciate the work you put in regardless of what you're being paid.
There's nothing wrong with showing gratitude from time to time, even if it's for a for-profit corporation if you truly appreciate what they do.
every other company is really just a collection of people like you and me
That's cool and all, but wasn't the motivation for the first letter the lack of humanity from GitHub in communication with the userbase?
I don't think they deserve a cooing public letter to reassure them on the basis of humanity after they've decided to give "empty response or even no response at all" to what read like perfectly reasonable attempts to communicate with them.
I'm entirely willing to use person-to-person social standards for a company. I'll start with a trust-but-verity attitude, because leveraging a double standard in customer facing business is often a way for companies to take advantage of customers. Once they show they're not interested: fuck 'em.
There's nothing wrong with showing gratitude from time to time, even if it's for a for-profit corporation if you truly appreciate what they do.