—— Update ——
This is not an issue anymore in iOS7. And there is better fix by Scott Jehl on github scottjehl/iOS-Orientationchange-Fix that works for iOS6.
—— Original answer ——
Jeremy Keith (@adactio) has a good solution for this on his blog Orientation and scale
Keep the Markup scalable
<meta name="viewport" content="width=device-width, initial-scale=1">
Then disable scalability with javascript until gesturestart with this script:
if (navigator.userAgent.match(/iPhone/i) || navigator.userAgent.match(/iPad/i)) {
var viewportmeta = document.querySelector('meta[name="viewport"]');
if (viewportmeta) {
viewportmeta.content="width=device-width, minimum-scale=1.0, maximum-scale=1.0, initial-scale=1.0";
document.body.addEventListener('gesturestart', function () {
viewportmeta.content="width=device-width, minimum-scale=0.25, maximum-scale=1.6";
}, false);
}
}