How can I disable a single checkbox in a 'checkboxes' FAPI element?
A clean way does exist in Drupal 7! Apparently, per this post, it's not yet documented.

function mymodule_form_alter(&amp;$form, &amp;$form_state, $form_id) {
  $form['checkboxes_element']['#disabled'] = TRUE; //disables all options
  $form['checkboxes_element'][abc]['#disabled'] = TRUE; //disables option, called abc
}


Another example.

You can also set #access function to FALSE, to completely hide the checkbox.