No, Printful can't disable any rates that are configured in Shopify, we can just add our own rates to the list.
To avoid offering a shipping option that we do not offer, you should disable any other shipping rates in Shopify, except Printful's.
Note that if your store has any products that are not fulfilled by Printful, you should leave some other shipping options in Shopify since Printful rates won't be returned for such items.