You can add some custom jquery to move the empty cart “outside” of the proceed to checkout button.
If you add the following to your themes functions.php:
wp_enqueue_script('my_custom', get_stylesheet_directory_uri() . "/js/custom-checkout.js", array('jquery'));
You can then create the custom js in the file specified (in this case theme/js/custom-checkout.js):
jQuery(function($) {
$("div.wcpgsk_empty_cart").insertAfter($("div.wc-proceed-to-checkout"));
});
At the moment, my empty button isn’t working, but at least it looks appropriate now.