This is fundamental. If Facebook messages are still to work as before, with a web interface, an archive etc. then you need to supply Facebook servers with a decryption key. You no longer have end to end encryption.
And I don't really see how they could get rid of the web features, it represents a massive number of FB Messenger users. This ties nicely with the older pressures from Zuckerberg to monetize WhatsApp and the resistance of the founders for security reasons, this most likely means access to the conversation plaintext.