If someone MITMs the connection between the CA and the website itself, then yes. I believe LetsEncrypt uses a variety of proxies around the world to measure the website, so there'd have to be a lot of successful simultaneous MITMs for that to work.
Ultimately you have to bootstrap trust from somewhere. Perhaps in future DNSSEC can be used to solve this problem (though DNSSEC is of course itself just another PKI).
Ultimately you have to bootstrap trust from somewhere. Perhaps in future DNSSEC can be used to solve this problem (though DNSSEC is of course itself just another PKI).