People may not like her, so think that it's not a big deal that she's not in it any more, but Sam and Mikaela and their relationship is important to making the movies believable. Plus, recasting wouldn't work IMO as the character is already established. I think it'll be tough to find someone, and get that chemistry built in such a short space of time. Or the other option, writing Mikaela out, won't make any sense to me, especially considering how the last one left of with them all loved-up. You can't just have a bunch of robots running around earth, as no-one will believe it. You need to have something that the audience can relate to, and in this case it's Sam and Mikaela's relationship, to make the whole thing believable.
People say she was a pain in the ass, yet conveniently ignore the letter from the crew member that painted her in a good light. And it's not as if she's the first actress to not like Bay and the way he is around females. Kate Beckinsale was critical of him after Pearl Harbour, and I read that the Australian actress from the first one refused to join the second one because of him.
At the end of the day, none of us know if she quite or was fired, just for me, everything points to her quiting. People say it's because she criticised Bay, but that was months ago, so why not just drop her then? Why wait till this close to filming? Plus, Shia recently criticised the movie and Steven Spielberg, yet he's still involved.