Form API Ajax - how to disable also form elements that will be changed, not only triggering element?
You can disable/enable some elements during ajax using this jQuery script:

// Disable filters on ajax call.
  $(document)
    .ajaxStart(function() {
      // Place here all elements that must be disabled during ajax.
      $("#path-to-the-element").attr("disabled", "disabled");
  })
    .ajaxComplete(function() {
      // Place here all elements that must be enablec after ajax.
      $("#path-to-the-element").removeAttr("disabled");
  });


Update. Some helper suggestions:


You can loop all inputs in wrapper element and disable each of them
using jQuery.each
You can see what is the class or id attribute of your generated
element html. Also you can add some special CSS class disable-on-ajax
to all your elements or wrappers that must be disabled on ajax. Then you will be able to handle them with one line of jQuery code.


Update 2

I can suggest one more solution. 
E.g. you have added class for your target elements 'disable-on-ajax'. 
Then you can write function that will be triggered on blur, select change, click etc.(You'll need to implements all target triggger checks). 
In this function you'll check if element has class "disable-on-ajax". And add second class "ajax-disabled". Then on ajaxStart you'll handle only element with class "ajax-disabled" 

You can populate form ajax-triggering elements, add property like ajax_wrapper="wrapper", ajax_event="event type" and then in behavior attach events