No, you're forgetting about Certificate Transparency, which protects against this attack.
You are entitled to revocation of any unexpired certificates for names over which you can demonstrate control. For Let's Encrypt for example you can automate this, simply make the API calls to demonstrate control (as you would for issuance) and then present the certificate that is to be revoked (it's in the logs) and ask their API to revoke it.
Maybe DNSSEC could be used here to help if ACME added a way to force DNSSEC-only domain validation.