Yes, you can exclude certain shipping services using this plugin:
woocommerce conditional shipping and payments V 1.3.3
This is a WooCommerce plugin for the full documentation please visit the official WooCommerce website.
In the example below l wanted to not allow certain Interparcel shipping rates if the cart weight exceeded 3 kg.
This was set up in the global setting.
Exclude shipping services at the product level.
You can also set up the plugin at the product level, you can add in the service codes, for instance using Australia Post this would be, AUS_PARCEL_COURIER for Courier Post.
For Fastway the service codes are