Have you considered not using Apache and mod_perl? I converted my personal website to lighttpd this week and I couldn't be happier. Now I am using FastCGI with perl and php scripts. Frameworks like Mojolicious and Dancer (and surely others) may benefit from using the built-in web servers and then using a reverse proxy to access them.
I'm not against a perl compiler per-se, but I don't think your current issue is with the lack of compiled perl code. You may want to also investigate PAR::Packer and Perl2exe from IndigoStar.