The code you have isnt getting the user id.
First you need to query the current user like what you have:
$current_user = wp_get_current_user();
But the bit you are missing is:
echo $current_user->ID;
So your code adpated will look like this:
$current_user = wp_get_current_user();
$pointsafterorder = $current_user->points - $woocommerce->cart->total;
update_user_meta( $current_user->ID, $current_user->points, $pointsafterorder );