You're completely right. I care about the free software movement from an ethical/freedom-preserving perspective, and I do think that many facets of the movement are too grounded in the details of how personal computer software in the 80s and 90s worked, rather than in the question of how to import the user-freedom-perserving ethos to services and data.

The question of how to create free-software-mediated online communities that don't involve storing user identity and data in a company's private database is critical. The user database, and what can be built upon it, is the single biggest reason people do use Github despite its flaws.

I don't think the community of GitHub matters as much as people keep saying here. I think each project has its own small number of developers, and getting all of them to move is much easier. It has a larger number of bug reporters and downloaders, who only interact with the project occasionally and are perfectly capable of doing the same thing anywhere else.