I'm afraid, there would not be a way to undo all notifications for emails, the user would need to remove those. However, you can change it so that moving forward this won't happen by changing your notification settings in ACP -> Members -> Notifications. You then would want to click "Reset members to default preferences" button.
You would not want to disable emails completely if your community is still operating, there are things like password reset emails, etc... which go out by email.