It might be something of a hack, but this works:
# Undefine disquswidgets to force a refresh also on ajax reload
window.DISQUSWIDGETS = undefined;
$.getScript("http://" + disqus_shortname + ".disqus.com/count.js");
Basically you trick Disqus into believing that the typeof is undefined, which will make it execute the same code again as it does the first time it's run.