I'm not too familiar with SharePoint beyond its general purpose, but you may be able to change the script reference to something like:
<!-- copy these lines to your document: -->
<div id="index_hype_container" style="margin:auto;position:relative;width:600px;height:400px;overflow:hidden;" aria-live="polite">
<!-- end copy -->
(basically removing the reference to the .hyperesources folder in the script's src).
Alternatively if you can post the hype document in a public URL then you can host the assets elsewhere and change the src to a http:// URL pointing to the document (or use an iframe).