Absolution Gap (Revelation Space, #3) by Alastair Reynolds

The Inhibitors were designed to eliminate any life-form reaching a certain level of intelligence - and they’ve targeted humanity. War veteran Clavain and a ragtag group of refugees have fled into hiding. Their leadership is faltering, and their situation is growing more desperate. But their little colony has just received an unexpected visitor: an avenging angel with the power to lead mankind to safety - or draw down its darkest enemy.

And as she leads them to an apparently insignificant moon light-years away, it begins to dawn to Clavain and his companions that to beat the enemy, it may be necessary to forge an alliance with something much worse…