In this instance making sure that you understand the service you are using (including intricacies like this), or keeping an extra backup of your own (a locally cloned copy of the repo), or for proper paranoia, both of the above.
No matter how much you trust github and those in positions of responsibility for the projects you interact with, if you don't know the exact details of the feature-set you can come unstuck due to operating under false impressions. Github has done nothing wrong, as that is how the service is intended to work and it is documented as such (though it would appear some of the documentation is incorrect or at least inconsistent?), but you still get an inconvenient surprise because of a misunderstanding.
A little paranoia can be very useful!
If you don't care about it that much, why do you keep it anyway?