I agree with you that is an issue for the package manager. A package manager should never have such a single point of failure. I know bower, for example, would fail (at least last I checked unless they added a caching system since then) but it at least can point to specific git repositories so it can be moved if necessary.
Honestly if anyone is working on something important enough where they must be able to rebuild at a moment's notice then they should either be checking in dependencies from these package managers or setting up their own copies of what they need. But that's like backing up; most don't realize they needed to be doing that until they have an issue so I can understand the anger when Github does go down.
