We can override the Ajax call to wp_ajax_get_tagcloud() and do a clean hack.
<?php
/* Plugin Name: Custom Admin Tag Cloud */
add_action( 'wp_ajax_get-tagcloud', 'ajax_tag_cloud_wpse_99497', 1 );
function ajax_tag_cloud_wpse_99497()
{
// PASTE ALL THE MODIFIED FUNCTION HERE
// http://core.trac.wordpress.org/browser/tags/3.5.1/wp-admin/includes/ajax-actions.php#L639
}
Restore your core files to its original state, copy the modified function inside the above container and create a plugin for it. And ready to go.
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