You should sort the list first... Then run the chosen plugin.
// sort list
var my_options = $("#my-dropdown option");
my_options.sort(function(a,b) {
if (a.text > b.text) return 1;
else if (a.text < b.text) return -1;
else return 0
})
$("#my-dropdown").empty().append(my_options);
// run chosen plugin
$("#my-dropdown").chosen({no_results_text: "No results matched"});
List sorting code pilfered from the highly rated answer here: