Yes, we plan to apply a few mitigations of this type. Part of the idea of the "Proof of Possession of a Prior Key" challenge is so that if a web server requests a cert for a domain with an existing certificate, we can ask them to prove that they hold that certificate.
Also, it seems possible that large scale DOS could be performed by applying for domains (via DNS hijack) before the owners do, causing significant administrative burden to recover from. I would suggest allowing simpler revocations within some multiple of the DNS TTL value for the domain.
I can also envision unscrupulous registrars pre-applying for LE certs for a fee, like $5.99 per month, and being very tardy and uncooperative about relinquishing control.
I can also envision unscrupulous registrars pre-applying for LE certs for a fee, like $5.99 per month, and being very tardy and uncooperative about relinquishing control.