Regarding deleting the key pair from the console. Is it only the reference you are deleting, as you showed that the key still exists in autherized_keys? If the keys are still there and you have your private key then I guess you can continue as normal, or what is actually happening when you delete the keypair reference in EC2 from the console?
You are deleting the reference to the public key that you no longer wish to use for future instances. While it doesn’t modify the instances as you mention, it removes the option