well, calling subs in Perl is not as expensive as people usually thing...

use Benchmark 'cmpthese';

my $a = 'foo bar doz' x 100;
$a .= ' hello '.$a;

my $sub = sub {
  /\bhello\b/; /\bhello\b/; /\bhello\b/; /\bhello\b/;
  /\bhello\b/; /\bhello\b/; /\bhello\b/; /\bhello\b/;
};

cmpthese(-3, { loop => sub {
                 for (($a) x 10) {
                   for my $i (1..8) {
                     /\bhello\b/;
                   }
                 }
               },
               sub => sub {
                 for (($a) x 10) {
                   $sub->()
                 }
               },
               inline => sub {
                 for (($a) x 10) {
                   /\bhello\b/; /\bhello\b/; /\bhello\b/; /\bhello\b/;
                   /\bhello\b/; /\bhello\b/; /\bhello\b/; /\bhello\b/;
                 }
               }
[download]

outputs...

         Rate   loop    sub inline
loop   4157/s     --    -5%   -16%
sub    4363/s     5%     --   -12%
inline 4943/s    19%    13%     --
[download]

and anyway, it's easy to modify my code to remove the subroutine call from the loop just moving the loop inside the sub:

open(MAP, "<$new_name_map_file");
while (<MAP>) {
     chomp;
     tr/A-Z/a-z/;
     @map_line = split (/\t/);
     $mapper{$map_line[0]} = $map_line[1];
}
close(MAP);

my $sub = <<'EOS';
sub {
  while (<IN>) {
  print "%";
  tr/A-Z/a-z/;
EOS

for my $name (sort keys %mapper) {
  my $qname = quotemeta $name;
  my $qrepl =  quotemeta $mapper{$name};
  $sub .= "s{\b$qname\b}{$qrepl}g;\n";
}

$sub .= <<'EOS'
    print OUT $_;
  }
}
EOS

$sub = eval $sub;
die if $@;

open(IN, "<input_file");
open(OUT, ">input_file.new");
$sub->();
close(IN);
clse(OUT);
[download]