So the solution is to not read from STDIN. Pass a file name instead of the file contents.

BEGIN {
   my %escapes = (
      "\\" => "\\\\",
      "\"" => "\\\"",
      "\n" => "\\n",
      "\r" => "\\r",
      "\t" => "\\t",
   );

   my ($escapes) = map qr/[$_]/,
                   join '',
                   map quotemeta,
                   keys %escapes;

   sub to_js_str_literal {
      for (my $s = $_[0]) {
         s/($escapes)/$escapes{$1}/g;
         s/([^\x20-\x7E])/sprintf("\\u%04X", ord($1))/eg;
         return qq{"$_"};
      }
   }
}
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my $js_script_qfn = to_js_str_literal($script_qfn);

print $JSWRITE <<"__END__";
var filename = $js_script_qfn;
load('jslint.js');
END
__END__
[download]

Well, don't know if scoping allows that exactly, but you get the idea.

Update: I suppose you could pass the file contents in the same manner.

print $JSWRITE map "$_\n",
   "var file = [",
   ( map "   ".to_js_str_literal($_), <$fh> ),
   "];",
   "load('jslint.js');",
   "END";
[download]