Good call - I can't make promises but I have moved this request to the next milestone.
To clarify, you basically don't want the "head html" to be in the source .html head, but get injected when the Hype document loads and be stored in the *_hype_generated_script.js file?
Basically the approach I would take would be to make an On Prepare For Display event on the first scene that gets triggered once and makes an element via the document.createElement() method that gets inserted into the head. Hype actually uses this technique to attach a CSS Reset and also include fonts in cases where they weren't found in the head, but there's sadly not any way to hook into it or get Hype to utilize it for other means.
An Export Script may be workable but probably a pain to do. You'd pretty much need to parse the .html file to extract what is in the head, and then have some sort of template substitution where you carefully perform a string replacement in the *_hype_generated_script.js file. I'm not sure I recommend this method; it is more of a "well, anything is possible with export scripts" approach.
Typically the solution to this problem is to simply include your Hype animation in an iframe, so it can contain all the head information.
I did see @MaxZieb just came out with this helper:
I haven't looked into how it works, but it sounds like it might fit your needs?