FB, via the WhatsApp app, have access to your unencrypted messages before the app encrypts them and sends them on. So, there's reason to worry now that FB is in full control. I have no doubt they'll extract data from your conversations and inject targeted ads.
Edit: Am I wrong? Do they not have access to the plain text?
From WhatsApp themselves [0]: "WhatsApp end-to-end encryption ensures only you and the person you're communicating with can read what's sent, and nobody in between, not even WhatsApp. Your messages are secured with locks, and only the recipient and you have the special keys needed to unlock and read your messages."
Similarly it needs decrypted on the other side and displayed to the other user, at which time the app again has accesd to clear text versions.
I don't believe there's any way to encrypt the message before the app sends the message / while it is displaying to the recipient
WhatsApp tells their users and more importantly the US Gov they do not have any access to the message content itself. For this attack surface to be an issue, that would mean WhatsApp is telling a bold faced lie, secretly exfiltrating the plaintext to a 3rd party, and doing so without getting caught by any black-box auditing.