Crossfire by Nancy Kress
Crossfire is the story of a human colony started by Jake Holman, a man trying to escape a dark past. As this diverse group of thousands of people comes to terms with their new lives on a new world, they make a startling discovery: primitive humanoid aliens. There are only a handful of isolated villages, and as the colonists gather more information, the evidence seems to indicate that the aliens aren't native to the planet. When the humans finally learn the truth, they find themselves caught up in an interstellar war between two very different species of alien. In the end, a handful of humans, led by Jake, must choose sides. The fate of not just their own home, but all of humanity, hangs in the balance.