Backtrace
Let's first check where this actually happens:
The meta box gets added on post.php and post-new.php screens.
# inside ~/wp-admin/edit-form-advanced.php
// TAGS:
if ( !is_taxonomy_hierarchical($tax_name) )
add_meta_box('tagsdiv-' . $tax_name, $label, 'post_tags_meta_box', null, 'side', 'core', array( 'taxonomy' => $tax_name ));
// CATEGORIES:
else
add_meta_box($tax_name . 'div', $label, 'post_categories_meta_box', null, 'side', 'core', array( 'taxonomy' => $tax_name ));
Then we move one file deeper into core to get to the definition/the meta box callback
// inside ~/wp-admin/meta-boxes.php
function post_categories_meta_box( $post, $box )
The categorychecklist tab is the one that holds the list. Inside the div, we got a function named wp_popular_terms_checklist($taxonomy);.
# inside ~/wp-admin/includes/template.php
<li id="<?php echo $id; ?>" class="popular-category">
<label class="selectit">
<input id="in-<?php echo $id; ?>" type="checkbox" <?php echo $checked; ?> value="<?php echo (int) $term->term_id; ?>" <?php echo $disabled ?>/>
<?php echo esc_html( apply_filters( 'the_category', $term->name ) ); ?>
</label>
</li>
» Conclusion:
This means, that we ain't got a real chance to intercept this on plain server side level with WP filters/hooks and PHP.
Doing something like...
add_filter( 'wp_get_object_terms', '__return_empty_array', 20, 4 );
... would simply disable the checked boxes completely.
will update if I got more information and (maybe a solution)