I'd like to add contacting Github support on the list. I once had a similar issue and after deleting the repo I asked them to flush their caches and delete backups. The support person redirected me to someone on the technical staff. They confirmed with me after verifying my identity and went ahead with the backup deletion. After that I pushed my fixed code to a new repo of the same name.

The entire process took less than an hour considering that it was 2pm in India when the issue happened and the support staff was most likely in the Americas.