By the way: why not using prefab code, like Apache::Admin::Config? Apache::ConfigFile is worth a look, too...

Update: here is the code. Instead of commenting out the offending section you can just simply remove it like this:

use strict;
use warnings;

# remove the <Directory "/opt/apache_2.0.48/icons/"> section

use Apache::Admin::Config;

my $conf = new Apache::Admin::Config "your_apache_conf.conf"
  or die $Apache::Admin::Config::ERROR;

my $section = $conf->select('section', 'directory', '"/opt/apache_2.0.
+48/icons/"');
$section->unlink;
print $conf->dump_raw;
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