What I did : On my production server, I create a config file (confthin.yml) for Thin (I'm using it) and add the following information :
environment: production user: www-data group: www-data SECRET_KEY_BASE: mysecretkeyproduction
I then launch the app with
thin start -C /whereeveristhefieonprod/configthin.yml
Work like a charm and then no need to have the secret key on version control
Hope it could help, but I'm sure the same thing could be done with Unicorn and others.