because I'm not using html generation functions from CGI.pm

Great, edit CGI.pm and delete them :)

Oh wait, thats called CGI::Simple but its not quite as up to date as CGI.pm

Hmm CGI::Alternatives not so much help for you

CGI.pm is about as light as it gets, even with all that html stuff you're not using ...

just because you're using CGI.pm doesn't mean you're limited to a non persistent environment like cgi/cgi-bin, you can easily go persistent with CGI::Emulate::PSGI if your code follows the best practices of scoping as per CGI to mod_perl Porting. mod_perl Coding guidelines