Perl hasn't become popular because of CGI, but because it is usefull. Every language has shortcomings, all areas of life have idiots and fascists and snobs. PHP is catered for web developlment. So what. Perl does all that and more.
I just want to say amen brother. We use Perl a great deal. In some cases the CGI module was useful. I don't know where I would be without Perl helping me manage the network.
There might be a "holy war" over which is the best web based language.
Perl is much too useful of a language to suggest its death because of CGI.