You could change your methodologies a bit, and enable PerlTaintCheck On in your httpd.conf (assuming an Apache server here), and then set the handler for files of type .plt to be tainted perl scripts (untainted?) and files of type .pl to be normal perl scripts.

Or, you could do it like I do, and enforce all perl scripts to run in taint mode, with PerlTaintCheck On on globally in httpd.conf.