.bind("load_node.jstree", function (e, data) {
          $(this).find('li[rel!=file]').find('.jstree-checkbox:first').hide();
      });

"types" : {
                "types": {
                "disabled" : {
                      "check_node" : false,
                      "uncheck_node" : false
                    }
                }
            }

$.jstree._reference('#tree').set_type("disabled", "#node5");

$rel = ( 'if the checkbox need to be pre-checked' )? 'rel="disabled" class="jstree-checked"' : '';
            echo '<li id="checkbox_id" '. $rel .'>';

.jstree({
                    "types" :
                    {
                        "types" : {
                            "disabled" : {
                                 "check_node" : false,
                                 "uncheck_node" : false
                            }
                        }
                    },
        "plugins" : ["themes","html_data","ui","crrm","types", "checkbox"],
                    "checkbox" : { "two_state" : true },
    })

#my_item_id .jstree-checkbox {
    display: none;
}