(Note that I am not a lawyer.) From the GitHub Terms of Service, paragraph F.1:
We claim no intellectual property rights over the material you provide to the Service. Your profile and materials uploaded remain yours. However, by setting your pages to be viewed publicly, you agree to allow others to view your Content. By setting your repositories to be viewed publicly, you agree to allow others to view and fork your repositories.
In other words, GitHub itself has nothing to do with how you license your code. So you can decide to stop publishing your source via GitHub, but everything that has been forked and cloned from it up to that point is of course still "out there" under the open source license you originally used.
The same holds for other people's contribution to the project: whatever was permitted by the original license remains, so it is between you and the other contributors. GitHub has little to do with it.
As to the updated question:
It is safest to assume that anything you put on the web is out there forever. GitHub allows you to browse the source code through the web. It seems that GitHub's robots.txt asks crawlers to stay away from the source code, but there's no guarantee that they will do this. I can easily imagine Google Code Search starting to index GitHub, for example (if they're not doing that already.)
Bottom line: once the source is public, you can never make it private anymore.