While it is true that the security of the script is determined not by the language but by the programmer, I would argue that it is easier to write secure scripts in Perl, because it has neccessary features to make this task easier.
Contrasting Perl to PHP, there is a wholly different culture of coding. PHP used to do everything with global variables (ok, not anymore, but I still see a lot of PHP scripts written with globals=On). PHP does a lot for you so that it would not get in the way for you when you are creating webpages. I am not saying that PHP developes don't know what they are doing, but PHP seems to attract developers who like easy no-thrills programming of small web applications and don't always think about security.
Perl at least has the features like taint mode that helps with security a lot. I think if one chooses to ignore these security features then he better know what he is doing. Although is easy to ignore the security features and write insecure scripts in Perl, at least there are tools available for writting secure ones.