I don't think that this can be automated, however you can put this into wp-content/mu-plugins folder:
<?php
/*
Plugin Name: Block WooCommerce Activation
Description: Prevents WooCommerce from being activated.
Author: Your Name
Version: 1.0
*/
add_action('admin_init', 'prevent_woocommerce_activation');
function prevent_woocommerce_activation() {
// Check if WooCommerce is attempting to activate
if (is_plugin_active('woocommerce/woocommerce.php')) {
deactivate_plugins('woocommerce/woocommerce.php');
wp_die(
__('WooCommerce activation is blocked on this site.', 'block-woocommerce-activation'),
__('Activation Blocked', 'block-woocommerce-activation'),
['back_link' => true]
);
}
}
Once Enhance make post installation scripts available, it should be pretty easy to automate this.