The article does have some issues, but a compromised CA would certainly make MitM easier. Not passive, but certainly ssl-strip [1] / ssl-sniff options get much easier.
Pinning certs (HPKP) is too dangerous so very few people implement it. That means if I have a signing cert for any trusted CA, I can ssl-strip with ease. This really has nothing specific to do with Lets Encrypt however. Any trusted CA signing cert will do. Or even an unlocked server cert (missing constraints) will do.