Bingo. As far as the PC is concerned, humans can slaughter each other as much as they like, but once they threaten to extend their conflicts into the rest of the galaxy, they need to be stopped. (Rewatch the AFOS's quizzing of Sara, around 17 minutes into the episode.)
Somewhere in the OAV, somebody says that the head and the body have been getting closer to each other over the years, whenever there's too much fighting.
As others have said, the AFOS isn't programmed to make decisions completely on its own. Responsibility for the ultimate decision and judgment has been passed down in Sara's family through the aeons. Notice that Mao says at one point that the AFOS doesn't really want to kill everyone (and she seems to have some insight due to the blood transfusion and the rebirth ritual). Sara is possessed by the AFOS in the sense that she no longer sees things through human eyes, but it's still her, and her emotions, that are guiding the AFOS's actions.
I agree with all of this and to me it makes sense. It really is a good story because it shows how the people on earth, protoculture, and the zentradi are all related, which they touch on in SDF Macross but never explain it all. I like Zero. But the end when shin flys away just confuses me. It seems they went with the happy ending instead of a more realistic and tragic ending. To me shin would have been a great hero if he did die in the end to save earth.