There's not currently an unregister_post_type function in WP, but it's quite simple to do with the code provided by Nacin on WordPress Trac:

unregister-post-type.php

<?php
if ( ! function_exists( 'unregister_post_type' ) ) :
function unregister_post_type( $post_type ) {
    global $wp_post_types;
    if ( isset( $wp_post_types[ $post_type ] ) ) {
        unset( $wp_post_types[ $post_type ] );
        return true;
    }
    return false;
}
endif;

unregister_post_type('my_custom_post');