Interesting query, OP.
The aim of true social commentary is identifying a social problem and rhetorically drawing attention to it. The focus there is the social problem. I'd rather this movie be character driven than driven by the film-maker's sociopolitical agenda. I think it would turn off summer movie goers hoping to see bats and supes to see instead a focus on heavy handed critique of society.
What they could do (and what I hope for) is keep the focus the characters and have them deal with a world that is similar to ours. There are certainly social factors that would come into play, but they are only being implemented because they make for character drama.
I think it's also important, considering that this movie needs an international and domestic audience in order to bring in maximum profit, to avoid demonizing any one nation. If they're going to show that certain nations want superman for their own military dominance, show a few nations, not just the USA or nations that are currently in opposition to the US. I don't think there's anything wrong with showing superman in war-like scenarios or even in Middle Eastern countries, but I hope they're sensitive to how each side is portrayed and remember that this is being shown to highlight how people react to Superman and not to admonish social conditions. There's no need to make things uncomfortably close to real-life. Let any social scenarios be inspired by things that really happen to give a sense of "This is a world like ours" but don't make exact parallels. This just isn't the movie for that.
Having said that, there's some really interesting places for them to go with these characters in terms of fantasy politics. A being like superman in particular would shift the world power balance in obvious and rapid ways that have never been encountered before. He's a free agent that reports to no one besides himself. There is no other being on the Earth that can say that. Everyone else is ruled in a sense. When Superman stands up for someone, it's like he's momentarily extending that invincibility and freedom to someone else because he rescues them from conditions imposed on them by individuals or rulers/governments. He gives power to the common people where governments and kings take it away. Such an ability would likely be simultaneously hated and revered. The leaders of the global super-powers are nothing more than figure heads to Kal-el and if he obliges them, it's in an effort to be kind and polite, but not to show subservience. It would be very interesting to see all the nations of the world either try to woo him or end him.
Certain corporations might not like superman interfering with long-standing kick-backs made to help the rich get richer and the poor to shoulder the burdens. These are things that happen across the world and could be easily addressed without the film appearing to advance any country-specific political agenda.
Superman is also a proponent of fairness and provides aid globally. It might make sense that some folks who assume (or know) that he's American may not take too kindly to him choosing to favor any one nation.
I can only imagine the kind of hateful dialogue they could write for Lex as he tries to spin superman's attempts at fairness against him:
"Does no one else see the irony in the idea that an alien who wears our colors and led destruction to our cities chose to side against us today?"
"He bends to no one. Some people treat him like a deity. Did you know that? He is a God and not one of those Gods that exists conveniently contained in temples and texts and has only as much power as humanity gives them. An living, breathing God that enforces his will on us and evades our punishments each day. Can you live like that? Do you remember freedom? Do you remember the days when humans decided for themselves what right and wrong means?"
"You're really out of place here, you know. Humanity neither needs nor can stomach a savior. Your image of us exists only in fairy tales. We simply do not have the fortitude to live next to our better. We will never be able to accept that we have someone living among that is willing to do what you do. We have to destroy such things because we can never be like you. We make war how we want, hate what we don't understand and even what we do understand on occasion. We most certainly hate anyone who dares invite us to walk a path requiring us to be something greater because that's when we learn that we were never as great as we always thought we were."
"We're really very similar, Mr. Wayne. Don't pretend that we're not so that you can sleep at night when we both know you already have may reasons to stay awake. You were right there with me, right there with all of them."
I can definitely see Lex using any negative reactions to Superman as examples of conditions and limitations that all humans are bound to. Naturally, Superman will focus on the opposite and knows that people are as capable of good as he thought they were.