You can absolutely "delete" a protocol if you own the Solana program.
It's not deleted in the sense that all of its history is still on the blockchain. But it is deleted in the sense that the account storing the Solana program no longer exists / is empty and you cannot interact with it. In fact, if you haven't immutably deployed a Solana program, you are heavily incentivized to delete it if it is unused, because then you can recoup the Solana you posted as rent to upload the program in the first place.
It's not deleted in the sense that all of its history is still on the blockchain. But it is deleted in the sense that the account storing the Solana program no longer exists / is empty and you cannot interact with it. In fact, if you haven't immutably deployed a Solana program, you are heavily incentivized to delete it if it is unused, because then you can recoup the Solana you posted as rent to upload the program in the first place.