Well a loss of control of your own data on someone else's service isn't a feature and should be something you should be expecting (create backups of your own data more often), yet as soon as everyone takes the 'free' upgrade bait on a third-party service, then 'all bets are off' including Github.
Seriously for organizations, you're better of in self-hosting your own projects on-premise with open-source alternatives like GitLab (recommended), cgit or even Gerrit to avoid nonsense like 'centralising everything to GitHub' in the long term. [0]