Agreed. Why not have a couple of Starfleet captains working together, trying to solve a problem, and the problem just keeps escalating?
What ever happened to the "rumor" that there would be a (female?) Starfleet captain in the film? Perhaps this is her crashed ship, and the Enterprise is on a rescue mission.
Maybe this is one of those "starfleet ship wanders into a someone else's war and becomes a casualty" stories -- Boutella's character's race versus Elba's character's race.
I do remember rumors of a character like that (a female captain that would match wits with Kirk) earlier this year, around the same time as rumors were going around of McCoy's ex-wife appearing, and that Bryan Cranston was in talks to be the villain.
Obviously the Cranston thing never happened. However, even though she's not in Starfleet gear, there's still no reason to believe Boutella can't be the captain of a ship (and not necessarily the crashed one) and isn't just a native of the planet where a ship has crashed. For all we know, Lydia Wilson was added to be McCoy's ex, but I doubt it.