Keeping your entire server-stack up-to-date, making sure you have SSL, using strong encryption for logging-in, hashing the passwords, making sure your server can only be reached via SSH, adding firewalls, filters, etc. etc.
Then some hacker in Eastern Europe comes along (or some beginner at the NSA/GCHQ) and finds out that your .git is exposed and somehow gains all vital user-data and admin data.
Being bashed with a boulder repeatedly would probably be less painful than the torture of knowing "I did it all, but they got me with an HTTP request... because nobody thought of double-checking what our VCS is doing".
How many other glaringly obvious mistakes might be out there right now? I can only imagine.