Remember when people used to sign (and/or encrypt) their emails with PGP/GPG? I'm not aware of a way to do that in gmail in any realistic sense.
I do remember, however, many early webmail clients barely supporting even small attachments. Some didn't support multipart.
Eventually, as webmail providers improved, the userbase decided the trade-off of losing the low-level access for the usability advances was worthwhile. I think email is an apt analogy.
GitHub is the first highly-successful incarnation of its kind. There are already credible competitors (albeit with much smaller user counts), and there will be more. GH has made a business decision on what features they spend time on. Other competitors will arrive at different decisions.
Developers, along with popular open source projects, will go to the providers that support their needs.