I agree that this aspect of the game is difficult to adapt to. It's hard to avoid civlian casualties, and although I don't pretend to be an expert on collateral damage, I'm sure that history suggests that civilian casualities are a hard reality of warfare.
However, the game addresses a crucial problem with past games in the genre: a lack of real consequences for civilian deaths. In the real world, there would first be a highly psychological quotient to be considered as agents see civilians die. There's a strong moral imperative for agents to save civilians, and the game does attempt to address this through harsh defeat conditions. Second, there's an even stronger political significance of civilian deaths. Although it's not necessarily practical, the real world assigns a profound value to civilian deaths. Therefore, I think there needs to be a way to make the preservation of civilian deaths paramount, without crippling the overall playability of the game.
I feel so incredibly indebted to the developers that I am humbled by the idea of offering my own suggestions, lest anything I say be construed as criticism. Let me then only suggest that the developers may find another way to employ rates of civilian casualties to penalize or reward the player. I do believe that friendly fire is indeed a serious problem politically, and could be punished with game defeat for excessive friendly-fire deaths. Beyond that, perhaps there's a way to apply a percentage to determine game defeat, such as if the percentage of civilians lost vs. saved reaches a certain level and does not go down within a probationary period, the PHALANX unit is suspended. This seems to mirror historical treatments of the issue. My compliments to the developers, and my sincere wishes that my comments here are a contribution to, not a detraction from, the most exciting game development I've seen in a decade.