Is there any way to move config app (app/config) above the app folder? I want to deploy app folder without override config files on multiple instances of my app.
I am not sure if that is possible. What you can do is adding a (set of) custom config(s) to you config.php's always_load section. You can add custom paths so that it can be loaded from any file, even outside of your application.
While this (partly) solves your problem, I might have a better solution for you:
You can configure your application per environment. APPPATH/config/production/*.php will override your default configuration. If you don't want to version control this folder, you can add it to .gitignore. If your deployment process is smart enough, you can configure to preserve configuration files between deployments. To activate production environment, you need to set the FUEL_ENV environment variable to production.