// Recursively delete a folder including all it's files and subfolders
// https://stackoverflow.com/a/18838141/701049
function recurseRmdir($dir)
{
    $files = array_diff(scandir($dir), array('.','..'));
    foreach ($files as $file) {
        (is_dir("$dir/$file") && !is_link("$dir/$file"))
            ? recurseRmdir("$dir/$file") : unlink("$dir/$file");
    }
    return rmdir($dir);
}

global $wpdb;
$user_ids = array_column(
                $wpdb->get_results('SELECT ID FROM ' . $wpdb->prefix . 'users', ARRAY_A),
                'ID'
            );
$basefolders = array(
                trailingslashit(WP_CONTENT_DIR) . 'uploads/avatars/',
                trailingslashit(WP_CONTENT_DIR) . 'uploads/buddypress/members/'
               );
foreach($basefolders as $base)
{
    $uid_folders = array_diff(scandir($base), array('.', '..'));
    foreach($uid_folders as $uid)
    {
        if(is_numeric($uid) && is_dir($base .'/'. $uid) && !in_array($uid, $user_ids)) {
            recurseRmdir($base .'/'. $uid);
        }
    }
}