At one point, I wrote a scrolling-style EPUB reader entirely in JavaScript as a Safari extension (mainly as a gag and to prove that it could be done), and except for the fact that it took many, many seconds to unzip the ZIP file, it did actually work, mostly.... But for your sanity, I don't recommend that approach.
I'd go with something much simple. For each source HTML page, create a static copy of that page in which you throw the book's TOC into a div and float it left, and throw the source HTML page into another div with a wide left margin.