If the product people at GitHub don't understand the sales/marketing impact that GitHub's free offerings have on its paid offerings, then they need to hire new product people.

I think it's plausible that the authors of the "Dear GitHub" open letter already realized the truth of Julian's response, which is why they posed their request in the way that they did.

This gives GitHub three choices. They can react positively, remain passive, or react negatively. If they react negatively, they have the risk of a PR shit-storm, which will negatively impact new customer acquisition. If they remain passive, they risk the chance that the attention to this campaign will grow and their reputation will decline. This will negatively impact new customer acquisition.

However, if they react positively, they show good will toward consumers of their free offering, and they show would-be paying customers their willingness to improve their services. This will positively impact new customer acquisition.

Were this request not made in the open, GitHub would not need worry about any of these outcomes, and would therefore not be forced to react.