It genuinely surprises the shit out of me that people haven't created a "middleware" layer that treats GitHub as its backend / source of truth, but everything gets routed through a custom domain. E.g., spin up this glorified reverse proxy on Heroku, and now example.com/bugs is really just example.github.io/bugs, which is a page with all its form actions pointing to the Heroku service acting as a go-between for managing github.com/example/whatever/issues with full backups, etc.
It's probable that in that instance they could just pay for GitHub datacenter or whatever Microsoft chooses to name the new evil plan. But Microsoft has little reason to turn evil again (open-source projects generally have little money and won't spend it on source control/issues when there's a free competitor), as we're at a crossroads where nobody needs Microsoft software anymore (iOS/Android/Mac/Chrome OS for personal computing, Google/Amazon for cloud), so they need the advertising for their cloud. Therefore, $500K per year or thereabouts to host all of the open-source code on GitHub and provide some amount of CI minutes is worth it to get people to ask for GitHub/Azure at work.