Most themes used comments_template to include their comment areas. It’s completely full of filters, one of which is the include file (usually comments.php) that you can hijack to include a file from your plugin that contains all the stuff for facebook comments (or nothing if you just want to disable comments.
Example:
<?php
add_filter( 'comments_template', 'wpse35363_comments_template' );
function wpse35363_comments_template( $file )
{
return plugin_dir_url( __FILE__ ) . 'path/to/your/file.php';
}
As far as general settings and per post settings, those are stored in wp_options and wp_postmeta respectively. Take a look at how the default comments compat file looks and you should get an idea about how you can do this in your plugin.