I think you should make an AJAX part in your plugin that would output the exact piece of HTML that you want and link to it instead, e.g.:
$pagenav = cot_pagenav('plug', 'r=pagesbyuser&id=' .$id . '&c=' .$c, $d, $totalitems, $cfg['plugin']['pagesbyuser']['pages_perpage'], 'd', '', true, 'pagesbyuser');
You might also want to replace 'd' with something else in the variable name to avoid conflicts with other plugins.