Are you familiar with how certificates and CAs work in general? You don't receive a certificate from the CA, they just sign and attest that the one you made is owned by you. The ways CAs go bad is not breaking any crypto but by signing a certificate that you don't own. This vulnerability is well known and LE takes industry-leading steps to mitigate it via the certificate transparency program which is a permanent audi…
From my understanding of the certificate transparency program does not mitigate the threat of them simply not disclosing a certificate they signed. Ultimately this still gives them MitM capabilities as long as they control the traffic or am I mistaken?
You may find this useful: http://www.certificate-transparency.org/how-ct-works