There was a whole arc where different government officials argued over how to resolve the situation. There was a coup and everything!

There is no way to tell a story about a country without talking politics. The only thing that differentiates one country from another is how they do things. These "ways of doing things" are called policies. Deciding on which policies are good and which are bad is known as politics, fairly straightforward. If you are not talking about politics, you may as well not talk about the countries in your story.

As for your question, of course you can write a story in a way where there is an abstract faceless "higher-up" figure, we've seen these, but the moment you try to create an actual character to represent the government, it will unavoidably get political when you see that character interacting with others in the story.