I am generating (X)HTML that contains some JavaScript, and the scripts often contain characters that are not XML. Is there a way to still use scala.xml for this stuff?

Yes there is. This task is so common nowadays that we decided to support it using a special Unparsed. We even tweaked XML syntax for it, with the xml:unparsed tag

object scriptgen {
  def main(args:Array[String]) = {
 
    // syntax error in Scala
    //val wrong = <script><!-- if(1 < 2) alert("scala.xml rocks"); --></script>
 
    // syntax error in JavaScript: the < will be escaped to &lt;
    //val wrong = <script><![CDATA[ if(1 < 2) alert("scala.xml rocks"); ]]></script>
 
    // 1. solution wrap in a comment
    val x0 = <script><!-- if(1 < 2) alert("scala.xml rocks"); --></script>
 
    // toString(true) preserves comments
    Console.println(x0.toString(true))
 
    // 2. solution, use xml.Unparsed to include verbatim
    val x1 =
      <script>
         { scala.xml.Unparsed("if(1 < 2) alert(\"scala.xml rocks\");") }
      </script>
 
    Console.println(x1.toString)
 
    // convenience for 2nd solution: use xml:unparsed 
    val x2 =
          <script>
            <xml:unparsed>
                  if(1 < 2) alert("scala.xml rocks");
            </xml:unparsed>
          </script>
 
    Console.println(x2)
  }
}

Why are CDATA nodes not preserved?

    <script>
    // <![CDATA[
      foo && bar
    // ]]>
    </script&gt;

    <script>
    //
      foo &amp;&amp; bar
    //
    </script>