Yeah, that's a good point. You'll need to get rid of the left-recursion. To do that, you'd need to get rid of binary_op and subexpression in your subexpression rule. Next, you'll need to factor out all of the paren stuff into a single rule, and then use that rule within the binary_op rule instead of subexpression. Here's an example:

paren:    '(' binary_op ')' { \$item [2] } # parens belong here, and o
+nly here!
         | subexpression
        
subexpression: function_call
              | var
              | literal
              | <error>

binary_op     : paren (op paren { [ \@item[1..2] ] })(s?)       # any 
+parenned expression will sink down here
                { [  \$item[1], map { \@\$_ } \@{\$item[2]} ] }
[download]

I wrote an article on eliminating left recursion in P::RD a while back: Eliminating Left Recursion in Parse::RecDescent

BTW, got a copy of your book recently. Nice one. ++ to you for sure. :-)