Highlight Field Errors with an Ajax Form
Not as hard as I thought, but for anyone else trying to solve the same issue, you need to get all the relevant fields from form_get_errors() and add the error class to the same - note I also clear the previous errors:

if (null !== form_get_errors()):
  $commands[] = ajax_command_invoke('#myFormDiv .form-item.error', 'removeClass', array('error'));
  $commands[] = ajax_command_remove('.alert-dismissable');
  $commands[] = ajax_command_prepend('#myErrorDiv', theme('status_messages'));
  foreach (form_get_errors() as $field =&gt; $message) :
    $commands[] = ajax_command_invoke('.form-item-'.$field, 'addClass', array('error'));
  endforeach;
  return array(
    '#type' =&gt; 'ajax',
    '#commands' =&gt; $commands,
  );   
endif;


Note that your $field will be dependent in what you've set in your validation function, so you might need to do some funky things to make sure '.form-item-'.$field is finding the right div.