Consequences, by Kristine Kathryn Rusch
Number three in the Retrieval Artist series by Kristine Kathryn Rusch... The first book is here, the second here.
This one is a bit of a departure from the first two since it doesn't really involve aliens. There was a civil war on a colony planet more than a decade ago, and certain people ended up disappearing since they were under death sentences. The power structure on that planet has since changed and pardons have been issued and everyone can supposedly come out of hiding.
Miles ends up retrieving one of those people and there are all kinds of consequences steming from that decision that go all the way back to the reason they disappeared in the first place. A number of people die and would they have if he hadn't retrieved that person?
A lot of the core story ends up being about the lengths people will go to to get their desired result. Very much a "do the ends justify the means" kind of thing.