Indeed. However, it's important to note that even if someone does MITM letsencrypt.org, they only see your public key and CSR. The private keys never get sent over the wire, so you don't risk leaking your private keys. However, a MITM could issue you a fake certificate that doesn't chain back to the Let's Encrypt root. This risk isn't any more than the way most CAs do it now (they email you the signed certificate).