It is better to process HTML as a template than to build nodes via JavaScript (HTML is not XML after all.) You can keep your IFRAME's HTML syntax clean by using a template and then appending the template's contents into another DIV.
<div id="placeholder"></div>
<script id="iframeTemplate" type="text/html">
<iframe src="...">
<!-- replace this line with alternate content -->
</iframe>
</script>
<script type="text/javascript">
var element,
html,
template;
element = document.getElementById("placeholder");
template = document.getElementById("iframeTemplate");
html = template.innerHTML;
element.innerHTML = html;
</script>