As a CA, Let's Encrypt should only be issuing certs to second level domains. If they want to issue one to a subdomain below that, there should be a check that the second level domain approves.
What about .co.uk ? Or the various other TLD that are 2-level deep already ? I believe it's impossible to implement this properly.
One of the main features of DNS is the ability to delegate authority for a zone. You use a NS record on a valid name that where you have authority to indicate that some other server is authoritative for a given subset of your zone.
If you bought example.com, you can create DNS records like
subdomin.example.com. 172800 IN NS ns1.example.com
to indicate that ns1.example.com is the authority for the entire subdomain.example.com zone. This includes all further nesting of .subdomain.example.com.Instead of guessing* who is responsible for a zone, you should simply ask the nearest upstream zone authority.
Also, relying on lists is almost always the wrong solution - if your security requires you to successfully enumerate something, you are doing it wrong. ( http://www.ranum.com/security/computer_security/editorials/d... )