There's not an automated solution to do this right now, though is something that should be possible with the Hype Export Scripts technology.
There's pretty much two aspects it sounds like you need, and there are some solutions on the forums to both:
1. inline all javascript
This is possible via an Advanced Export set to inline data+loader, and then manually pasting the contents of the Hype runtime file. Please see the tips here:
2. base64 encode image assets/inline SVG
This is a bit trickier; you will ultimately you will need to replace your images in the Hype document with elements using inner HTML that have the base64 data URI.
There's an extension that can help with this process: