Yes you can. Dotdeb's php-fpm.ini even includes this line by default:

    ; To configure the pools it is recommended to have one .conf file per
    ; pool in the following directory:
    include=/etc/php5/fpm/pool.d/*.conf

Then you could configure ENV inside FPM pool using the env directive:

    env[DB_HOST] = localhost
    env[DB_USER] = foobar
    env[DB_PASSWORD] = foobar

...and use something like this in e.g. Wordpress config:

    define('DB_NAME', getenv('DB_NAME'));
    define('DB_USER', getenv('DB_USER'));
    define('DB_PASSWORD', getenv('DB_PASSWORD'));

The biggest caveat is you MUST disable phpinfo()

    php_value[disable_functions] = phpinfo

Otherwise these ENV will shown up in any page that calls phpinfo();