You can use the DirectoryIndex apache directive to set the default document. Something like:
DirectoryIndex index.html index.htm index.cgi
would execute index.cgi (assuming apache has been configured to execute .cgi files (Options ExecCGI)) if index.html and index.htm can not be found. The index.cgi could then check the QUERY_STRING to determine whether the person wants to execute script.pl or get the default html page.