I’ve found a dirty way for now..
This is only possible to hack the plugin codes (don’t forget this customization will be deleted after first update)..
Open class_frontend.php file and find function fbcommentbox($content) {
line and put below code right after this line (before the $options = get_option('fbcomments');
line);
global $post;
if ($post->post_type == 'custom_post_type') return {$content;}
Update the file, then you’ll not see plugin for custom_post_type post types.