Sure. The two most popular examples are the C Plus Equality repo and the Operation Disrespectful Nod repo, which were a satirical programming language and a Gamergate resource list for contacting advertisers, respectively.
It's not proof that _he_ necessarily removed it, but considering it wasn't brought down by the actual repo maintainer, and that any repos created to replace it by other users at the time were taken down as well, it's a safe assumption that someone at GH did.
There's several more sources regarding this, but I'm on a terrible mobile connection at the moment. Googling around will get you a bit more info for the story.
http://tech.slashdot.org/story/13/12/14/1618239/github-takes...
https://pipedot.org/story/2014-10-04/github-staff-jake-boxer...