I know perl better than php, so understand that I'm biased here.
Perl is a more mature language, and is significantly less vulnerable to exploits. It's more powerful as well. BUT it is harder to learn for sure. php makes scripting on Unix pretty much like writing ASP pages for a Microsoft server. But the bottom line is you can do stuff with perl that you can't with php - the converse isn't true.
I'm responsible for a Webserver that perhaps a hundred people have write access to, and everyone in the department (maybe 1000 people) can at least log in. Since the skill level of our users varies quite a bit, we limit what they're allowed to do. On our server we have php disabled simply because it's less mature and therefore more exploitable. php exploits still come out every month or two, and they tend to be "severe" bugs. BTW we don't allow unrestricted CGI access either; I have to vet most scripts before they're made live (except for a few users whose skill levels are good).
Edit: I should probably point out that in many production environments you can set all scripts to run under the specific user's permissions - so at worst they can only compromise they're own files. But in our particular setup that's not practical (except for a few virtual hosts that are on our system - in those cases we do that).
