Protecting shipping methods, billing methods, and coupon codes
Short version: It's not possible to protect shipping methods, billing methods, or coupon codes.
Shopify keeps a pretty tight leash on the checkout process itself, and third-party apps aren't permitted to get involved here at this time.
If you absolutely must set up different shipping or billing terms, your best bet may be to set up a completely new Shopify store.
If you want to dig into this further, get in touch with the Shopify support crew directly, at email@example.com.