This normally is not a problem. Those characters are only encoded as < or > if you use DOMDocument::saveXML(). If you use DOMDocument::saveHTML() those are just < and > in a <script> tag.
Example:
<?php
/**
 * PHP DOM and JavaScript with HTML entities
 *
 * @link http://stackoverflow.com/q/18487515/367456
 */
$doc = new DOMDocument("1.0");
$doc->loadXML('<head/>');
$javascriptCode = "\n  if (1 < 4) {\n    alert(\"hello\");\n  }\n";
$script = $doc->createElement('script');
$script->appendChild($doc->createCDATASection($javascriptCode));
$head         = $doc->getElementsByTagName('head')->item(0);
$scriptInHead = $head->appendChild($script);
echo 'libxml: ', LIBXML_DOTTED_VERSION, "\n"
    , "\nXML:\n", $doc->saveXML()
    , "\nHTML:\n", $doc->saveHTML()
;
Program Output (Demo (Multi-Version)):
libxml: 2.7.8
XML:
<?xml version="1.0"?>
<head><script><![CDATA[
  if (1 < 4) {
    alert("hello");
  }
]]></script></head>
HTML:
<head><script>
  if (1 < 4) {
    alert("hello");
  }
</script></head>