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.
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.
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.
If you made something public on GitHub that shouldn’t have been, it was immediately compromised, you just might not notice.