I don't know if this would work for the environment you're in (and who developed script.pl and what it does), but have you thought about putting the functionality of the script into a Perl module and just useing that module in your CGI script? In addition to not having to worry about the taint problems you're having, it should also be a little faster as you don't have to start up another Perl interpreter every time (and if you use mod_perl, the module wouldn't even have to be loaded every time).

I guess it just sounds kinda weird to me to call a Perl program from within a Perl program. :-)