This is what worked for me on iOS 6 (very slight adaptation of rmarscher's answer):
<script>
(function(document,navigator,standalone) {
if (standalone in navigator && navigator[standalone]) {
var curnode,location=document.location,stop=/^(a|html)$/i;
document.addEventListener("click", function(e) {
curnode=e.target;
while (!stop.test(curnode.nodeName)) {
curnode=curnode.parentNode;
}
if ("href" in curnode && (curnode.href.indexOf("http") || ~curnode.href.indexOf(location.host)) && curnode.target == false) {
e.preventDefault();
location.href=curnode.href
}
},false);
}
})(document,window.navigator,"standalone")
</script>