jstree disable checkbox

You will need to define a "disabled" type (using the types plugin) and then assign that type to the desired node.

Take for instance this "disabled" type definition:

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

and the type assigment:

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

More info on the types plugin can be found here and you can also check this google group with more info on disabling checkboxes

Hope it helps!