Not necessarily. There's enough soldier worship in American culture to really sell that angle in a protagonist whose intentions and/or cause are not necessarily honorable. It's extremely hard to do and most game developers try to avoid putting themselves in that situation (let's count the number of first person shooters set in the Vietnam War) but it's not impossible. As in films and novels of the same type, it really just requires the protagonist mostly owning the fact that they're probably fighting for the wrong side and may or may not be even be a good person, but then adopts a "fuck it, I wanna LIVE!" approach and fights on anyway. The story becomes less about morality or empires or some broader mission and a lot more about "Holy crap, there's a million people trying to kill me and how the hell am I gonna get out of this one?!"
What you're describing is generally only suited to telling the story of a foot soldier (basically, Finn's story.)
Iden Versio is elite special forces, which means she's already hip-deep in moral ambiguity from the off-set.
I'm not saying they won't go that route, but it doesn't seem like much of a character arc given the starting point.