A annoying part of JSF is that it will strip out all of your conditional statements. These conditional references are needed for IE bug fixes 99% of the time. The solution is a simple hack using the outputText component. This will treat the html entities as strings and convert them.
For example this outputText will render the html5shiv cdn.
<h:outputText value="<!--[if lte IE 8]> <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.2/html5shiv.min.js"></script> <![endif]-->" escape="false" />
Results
<!--[if lte IE 8]> <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.2/html5shiv.min.js"></script> <![endif]-->
Now once rendered the browser will be able to correctly interpret your conditional statements.