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

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

##</code><code>##

<?xml version="1.0"?>
<opt>
  <node>
    <val>1</val>
  </node>
  
  <node>
    <val>3</val>
  </node>
</opt>