Just instruct users to put it in the index.html, unless you're planning to make make this a full on git hook application like travis and allow it to write back to github. That would be cool, actually, since everything is already parsed with JS and runs in commonJS.
I guess we could add it to the readme, but that's true. This is a JS library and cannot be used without it. You're welcomed to add <noscript> in your gh-pages if that's the way you're using DocumentUp, but that's no an issue with the hosted version.