GitHub made a cardinal UX design sin here: never use a warning when you mean undo [1]. If they had given even a five minute grace period before starting the irreversible process of removing all the watchers, this wouldn’t have happened.
I’m not saying there isn’t a better way Github could handle this situation. Just that I do sympathise with the decision to cascade delete.
Stop sending notifications to watchers, and replace the repo in the stargazer's starred list with a "The following starred repos are currently private and cannot be viewed:" and make the stars be remove-only for a while.
If you made something public on GitHub that shouldn’t have been, it was immediately compromised, you just might not notice.