Perl can be used for both scripting and for programming. I think the argument is more about what is scripting and what is programming. Here's my view:

In my world, a script is just like a stage script - Actor A says this and does this, Actor B says that and does that. Except instead of people your actors are programs, typically unix utilities. They do (execute) and say (create output) things as you tell them to do with your script. As the script writer you're most concerned with orchestrating these interactions and controlling inputs and outputs to other peoples' programs.

Contrast with programming where you're concerned more with classes, subroutines, data structures, algorithms and the like. Sure, scripts touch on the above, just as a stage script shares elements with a novel, but not to the same extent. And certainly some projects involve both scripting and programming, and there's nothing wrong with a program calling a script on occasion, but that's not going to be its primary purpose. Sometimes the line between the two might be somewhat fuzzy.

Perl is the best language you can use for scripting, and in many cases the best language you can use for programming. There are more areas of deficiency on the programming side than on the scripting side - Perl 6 addresses many of them.