A small update to those out there running into this. I was able to hide the iframe by targeting IE with a sort of catch all IE conditional statement like this
<!--[if IE ]>
<style type="text/css">
@import url("/CMSPages/GetCSS.aspx?stylesheetname=ie");
</style>
<![endif]-->
With of course the creation of a stylesheet named ie
From there, it was simply a matter of using the following css styling option (for IE only)
filter: alpha(opacity=0)
and applying that attribute to each of the iframe ID's. Of course this makes updates to the menu all that much more troublesome, so if anyone has a more appealing solution I'm all eears.