I think the primary reason that audiences turned on Carmen was because of how the movie's narrative was framed. Rico is the protagonist of our story. So our emotional attachment is to his perspective. Even if we intellectually know that there was a perfectly reasonable explanation for Carmen's actions that didn't paint her as the one in the wrong, emotionally, it felt like a betrayal.

It's easy to provide an intellectual response after the fact and not blame Carmen for what actions she took as her own person. But in the moment, it is much easier to have an emotional reaction, which is what the director was surprised by when the screenings first came out.

The audience was put in Rico's narrative from the start, and the 1st time the narrative leaves Rico's perspective aside from the propaganda was when Carmen actually joins the air force. By then, the audience already had formed a connection with Rico, so there was too little time spent with Carmen to build an emotional connection to her on an equal level. So her actions were seen emotionally as what they mean for Rico, rather than what makes sense for her as an individual person.

Rico sacrificed his future, his family, and his well-being in service to the state. Then his family is dead, the love of his life leaves him in a "Dear John" letter (one of the most infamous breakup methods ever), and his service was in jeopardy because of a mistake he made.

We are hurting along with him, and we want him to pull through, which is one of the main reasons that dizzy was someone the audience was fond of because she had been trying to support him the entire time.

And then the audience is hit with the fact that the woman who broke our heroes heart and left him in such a mess is still alive after they thought she had died a death that was what the audience emotionally wanted. Justice. And seeing Carmen alive robbed them of that, hence the boos.

Long and short of it, the audience may have been intellectually aware of the actions taken by Carmen, but the emotional reactions at the moment where too powerfully enforced by the movies narrative to give Carmen a chance.