Why not use the same mechanism you use to scroll the main document window?
This behavior is intuitive, if slightly inconvenient in some cases, which is exactly the trade-off I'd have expected Apple to make. Requiring an unfamiliar multitouch gesture for a common operation strikes me as the kind of "let's do something cool because we can" geekery that got us middle-click-to-paste in X Windows.
I'm curious: what does the iPhone use to scroll an iframe in an iframe? Three fingers?