If you're shelling out to commands you think might snarf credentials, the environment is easy for them to pick it out of, but if they're running as the same user then they could probably read the secrets from the config file. If they aren't running as the same user, you need a way of passing in the secrets - and we tend to come back to environment variables..
The good practice here is just to reset the environment when calling shell commands, as he notes. It's not hard to do.