There's an easy fix for this problem. Just prevent page scrolling when popup is active.
Working jsFiddle
example: http://jsfiddle.net/Gajotres/aJChc/
For this to work popup needs to have an attribute: data-dismissible="false"
it will prevent popup closure when clicked outside of it. Another attribute can be used: data-overlay-theme="a"
it will color popup overlay div. That is a DIV that covers screen when popup is opened and prevents popup closure.
And this javascript will work on every possible popup:
$(document).on('popupafteropen', '[data-role="popup"]' ,function( event, ui ) {
$('body').css('overflow','hidden');
}).on('popupafterclose', '[data-role="popup"]' ,function( event, ui ) {
$('body').css('overflow','auto');
});