use XML::LibXML;
use strict;

my $file = (<DATA Or filename>);

my $d = XML::LibXML->new->parse_string(join "", $file);
for my $dead ($d->findnodes(q{/opt/node[val = "2"]})) 
{
  $dead->unbindNode;
}
print $d->toString;

Data____
<?xml version="1.0"?>

<opt>
  <node>
    <val>1</val>
  </node>
  <node>
    <val>2</val>
  </node>
  <node>
    <val>3</val>
  </node>
</opt>