Let's Encrypt is one of the best things that happened to the web recently. I wish we had more choices though. Relying so much on a single party is unnerving.
Do we have conclusive evidence yet that LE is not a honey pot? I mean, if I were the NSA...
1) the honeypot uses your private keys to MITM connections
Let's Encrypt doesn't handle your private keys. You generate them yourself, and submit a CRL to LE to get a cert issued. They have no knowledge of your private key.
2) the honeypot issues fake certs
Let's Encrypt submits a log of every cert issued, see https://crt.sh/ . To verify, it'd be pretty trivial to create a browser extension (if one doesn't exist already) that checks whether certs you encounter appear in the certificate log.