I had a similar issue with an old version of jCrop and created a custom destroy function. Here is the gist of it:
function crop_reset()
{
//Reset coordinates of thumbnail preview container
$('#crop_preview').data("coords.x", 0);
$('#crop_preview').data("coords.y", 0);
$('#crop_preview').data("coords.w", 0);
$('#crop_preview').data("coords.h", 0);
//Reset src of jcrop img and copies bound to page specific full size and preview divs
$("#crop, #crop_preview, .jcrop-holder img").attr("src", "");
}
function crop_start()
{
//Initialize and remove previous jCrop containers using load event callback
$('#crop').Jcrop({
onChange: showPreview,
onSelect: showPreview,
onLoad: hidePreview,
aspectRatio: 1,
setSelect: [0, 0, 50, 50],
minSize: [50, 50],
allowResize: false,
allowMove: true
},function(){$(".jcrop-holder").not(":last").remove();});
//Remove previous jCrop containers using timer if callback is not supported
/*
window.setTimeout(function noblank(){
$(".jcrop-holder").not(":last").remove();
}, 1000);
*/
}