You can't shove a <script> tag inside a innerHTML property and expect it to load. You could try using createElement() methods and then appendChild(), but I'm not sure the script would load that way either.
Personally with the script you have I'd just do this:
Code:
<div id="navbar_720x90" style="display: none;"><script language='javascript' type='text/javascript' src='http://blablabla.com/st?ad_type=ad&ad_size=728x90'></script></div>
<script type="text/javascript">
<!--
function init_banners()
{
document.getElementById('navbar_720x90').style.display = '';
}
init_banners();
-->
</script>