Perhaps this is a question of the use of the word "free". There's a narrow interpretation of it to mean "able to be said" and also "allowed or constrained by government". Twitter deplatforming this engineer would be fit the narrow flavor, and nothing written so far suggests that happened. Elon has not said the Twitter will have a free-speech-oriented employer-employee dynamic. Few if any workplaces have. I'd be very interested in hearing from people who think their management chain would handle it well, especially if they think their management chain would publicly pop off with the information level on topics that Elon appears to be.
I'm not on the side of a petty thin-skinned manager behaving like this at all. I just believe it is pretty much the common case that managers called out in public will fire you, so you'd expect it. Especially from Elon.
You can only think that as an unavoidable consequence if you assume the CEO's ego is more important than the company.