How do I replace a function, declared inside a plugin’s class, in functions.php?

This should work:

add_action( 'woocommerce_init', 'remove_wcpgsk_email_order_table' );
function remove_wcpgsk_email_order_table() {

    global $wcpgsk;
    remove_action( 'woocommerce_email_after_order_table', array( $wcpgsk, 'wcpgsk_email_after_order_table' ) );

}