How to remove a dangling commit from GitHub?

GitHub will periodically garbage collect any commits (and other objects) that can not be reached from a top-level reference (such as a tag or a branch or reflog). This means that over time (say in the next month), this object will disappear.

Pulling should generate a pack that contains only objects that are referenced so no one should get that commit as a result of a clone or a pull. For example,

$ git clone git://github.com/nylen/connectbot.git
Cloning into connectbot...
remote: Counting objects: 6261, done.
remote: Compressing objects: 100% (1900/1900), done.
remote: Total 6261 (delta 3739), reused 5980 (delta 3520)
Receiving objects: 100% (6261/6261), 3.04 MiB | 3.40 MiB/s, done.
Resolving deltas: 100% (3739/3739), done.
$ git cat-file -t 1cd775d
fatal: Not a valid object name 1cd775d

If you really need it to be removed immediately, you would probably have to contact GitHub Support.

Delete the repo or contact GitHub

Deleting the repo and recreating it without the bad commit seems to work if you can afford losing all issues. The data also disappears from the commit API (although push events are still visible). See also: https://stackoverflow.com/a/32840254/895245

If you can't afford to lose issue data, GitHub support can manually delete dangling commits. For example, when I uploaded all GitHub commit emails to a repo they asked me to take it down, so I did, and they did a gc. Pull requests that contain the data have to be deleted however: that repo data remained accessible up to one year after initial takedown due to this.

Their current help page says:

you can permanently remove all of your repository's cached views and pull requests on GitHub by contacting GitHub Support.

Maybe making the repo private will also keep the issues around and get rid of the commit, I'm not sure. You lose starts/forks for sure though. Not sure if after restore the commits will be gone or not. But at least you might be able to keep a private backup of issues.