Conditionally enable/disable #autocomplete from client side js
Ok I managed to achieve this after digging into misc/autocomplete.js

To disable the autocomplete you can do the following:

$('#edit-search').unbind('keydown keyup blur');
$('#[AUTOCOMPLETE-ELEMENT-ID]-autocomplete-aria-live').remove();
$('#[AUTOCOMPLETE-ELEMENT-ID]-autocomplete').removeClass('autocomplete-processed');


To enable the it again:

Drupal.behaviors.autocomplete.attach(document);


My js ended up as:..

// update search box text when search type is changed
$(SI_SEARCH.radio).change(function() {
  // get search type
  SI_SEARCH.search_type = $(this).val().trim();
  switch(SI_SEARCH.search_type) {
    case 'course' :
      // re-attach autocomplete
      Drupal.behaviors.autocomplete.attach(document);
      break;
    case 'university' :
      // disable autocomplete
      $(SI_SEARCH.search_form).next().removeClass('autocomplete-processed');
      $(SI_SEARCH.search_form).unbind('keydown keyup blur');
      $('#edit-search-autocomplete-aria-live').remove();
      break;
  }
})