The magic sauce would be CAA. This is under the assumption that all publicly trusted CAs respect CAA and have no bypass bugs (CAs probably aren't ... too far off target) and that they properly validate DNSSEC (good luck with that, I don't think there's even consensus on what the Baseline Requirements consider compliant).

Anyway, in this mostly hypothetical world where all of that works as intended, you could use a CAA record with just one or two CAs with which you have some kind of contractual relationship requiring out-of-band verification. Alternatively (and, IMO, preferable, since the controls are technical), you can use the ACME CAA extension[1] to lock down the validation methods to just DNS-based ones, or bind the the whole validation flow to a key. Let's Encrypt is working on this currently[2].

[1]: https://tools.ietf.org/html/draft-ietf-acme-caa-05#section-4

[2]: https://community.letsencrypt.org/t/acme-caa-validationmetho...