[Deff]

var el = document.getElementById('content_id');
var html = refs_proc(el.innerHTML);
el.innerHTML = html.replace(/<([^<>]*?script[^<>]*?>)/img,'&lt;$1&gt;');        // Что делать?

<div id='content_id'></div>


<script type="text/javascript">
var el = document.getElementById('content_id');
var html = '<b>Вася</b><script type="text/javascript">alert("Привет")<\/script>'
el.innerHTML = html.replace(/<([^<>]*?script[^<>]*?)>/img,'&lt;$1&gt;');
</script>