It isn't related to iframes directly. Iframes in mobile Safari are never scrollable. The div thing you suggest would have the same issue. If you are a web developer you likely have built a website that has this issue.
So my top-of-the-head guess of something that might avoid it based on what I thought the problem was from other HN discussions wasn't right. What a sin.
That doesn't invalidate my experience or frustration as an end user.