Note that this won't work.

The script is executed in a child process. Changes to the environment are only accessible to that process. Exported environment variables are accessible to all children processes, but not necessarily the parent. The environment variable changes done by script.sh will be lost as soon as script.sh exits.

The only way to get environment variables in this session is to parse them in as the other poster suggests. The alternative would be to use a shell script or something as your CGI (a wrapper, really), and have it source the conf.sh script first, followed by exec'ing your Perl CGI script.