Have a look here:
https://github.com/edwilde/iBooks-HTML-Widget-Boilerplate
This is a boilerplate specifically for building for iBooks, which apparently targets & fixes your problem specifically.
Another suggestion would be using an iFrame, something like:
<div id="container" style="overflow: scroll; -webkit-overflow-scrolling: touch;">
<iframe width="4000" height="100%" src="">
</iframe>
</div>