How would you go about making a repeatable, automated deployment if you don't store configuration information in source control to load into the environment variables?

Depends on what you're using for your deployments, for example if you were using Puppet you might use something like https://github.com/TomPoulton/hiera-eyaml

Sorry, how does this prevent you requiring configuration in source control, or are you just suggesting that those credentials should be encrypted?

Consul and Vault go a long way to achieving that.

https://consul.io/

https://vault.io

Doesn't this just push the problem up (down?) a level in the hierarchy? I mean, you still need to deploy these and configure them with the information the rest of your deployment requires right?

That link is talking about a problem with e.g. .htaccess and basic directory permissions, not a problem using git per se. But yeah, put that stuff in envars.