At the moment you can get that behaviour with "certonly --csr". You'll need to make a CSR file yourself. It'll drop your cert and chain files in the current directory. You'll still have an account key and some other ACME protocol housekeeping state in /etc/letsencrypt.

https://github.com/certbot/certbot/issues/2373 will track implementation a nicer version of that functionality; it'll probably be --no-lineages (lineages are Certbot's notion of a succession of renewed or updated certificates that replace each other; they live in /etc/letsencrypt/live, though you can put them somewhere else with the --config-dir option)