That isn't really fair. If you read the article, protonmail essentially supplied the FBI the recovery email of the account. This is metadata that protonmail must have that isn't encrypted by the user for obvious reasons.
Regarding the "MITM" for every email sent, this is related to their "bridge" software which allows regular IMAP/SMTP software to use Proton Mail. This software must edit the emails to encrypt them in their scheme.
This software is open source and can be inspected and/or built locally. https://github.com/ProtonMail/proton-bridge