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();