I was surprised by the lack of fixed headers/footers, too. They say it's coming, but in the mean time you can use iScroll without any side-effects:
And, as you say, use the 'fixed' CSS in newer Safari versions that support it.
Well, they say it's done by taking "advantage of native scrolling":
http://jquerymobile.com/test/docs/toolbars/bars-fixed.html
And there obviously is improvement over the previous version, in that, earlier there was some flickering of fixed elements on desktop view-port.
I stand corrected, and appreciate the effort jQuery team.
One instance, for example, was in having "fixed" header/footer on the web-app. The rendition of fixed elements would fade-out and fade-in again once user stopped scrolling. This really felt naive and I decided to do that part myself instead.
Obviously, now the situation has improved that we have property 'fixed' acknowledged on the iPad Safari. Will give 1.1 a look again, thanks to this heads-up!