The sad thing is, it isn't the tool (I don't really know, but I assume perl is a pretty good tool used appropriately), but the way it was used.
Absolutely. I've done perl development since '94 (my first script was for controlling a 9-track tape reader, and printing a report for paper logging). It's a great language, but it's expressiveness can get people into trouble. It's DWIM-iness is a double-edged sword.
What person thinks going into a completely windows environment with only windows system admins and decides to write perl scripts hosted on Linux box, I don't know. I guess when all you have is a hammer . . .
Sounds like you're the one holding the hammer.

FWIW, it's possible to run perl on Windows, too. If you're uncomfortable with the scripts being on a linux box, perhaps step one should be move them to a Windows machine, so that you can at least admin the machine.