I had previously been using iScroll plugin but wanted to drop it for the native behaviour.
The initial implementation was using
webkit-overflow-scr
This bug seems even worse with iFrames. I created a JSFIDDLE to demonstrate it (open http://jsfiddle.net/KMayN/9/ with an iOS 5.0.1 device) and I sent a bug report to Apple. Very curious: if you scroll, you'll see a blank (not rendered) content...but if you then zoom, the content appears! And so on... I will keep you up-to-date if they reply to me. I tried everything (scrollable iFrame with/without div container, container with/without scrolling, etc...), there are simply no way: we have to wait Apple for a bugfix.