GitHub offers and enterprise offering that you can host yourself. It's no better/worse than hosting your own version of JIRA, Confluence, and a git repository. That way you're not 100% dependent on github.com actually being up. As far as changes, you're right, but the changes are true with any product. At my last company, we did a JIRA upgrade which ended up being a nightmare for process because lots of things changed and were configured incorrectly. I guess I'm trying to say that what you're saying is true for any SaaS product you use and doesn't take away from trying to use GitHub, maybe not necessarily github.com, to run everything.