Just as The Doctor thinks he may have brokered a peace between humanity and the Silurian race, it turns out that Ambrose has killed one of the Silurians. This undermines the trust that had developed, and provokes an attack. The Doctor and friends are fortunate to escape.
The Doctor can be critical of human actions, but at the same time is a great advocate for the human race. When finding out about the murder, he exclaims that "you are so much less that the best of humanity". Yet in the same conversation he pleads with the Silurians on behalf of humanity. "You have to believe me - they're better than this." A powerful reminder of the God's high standards yet unlimited capacity for forgiveness.
Meanwhile, safely back on the surface, Ambrose and The Doctor have this conversation:
AMBROSE: You could have let those things shoot me. You saved me.
DOCTOR: 'An eye for an eye' was never the way. Now you show your son how wrong you were - how there's another way. You make him the best of humanity - in the way you couldn't be.
This is classic Jesus 101. Ambrose has done something terrible, and The Doctor's response is to forgive her - to save her. He offers her another chance - the opportunity to change her ways and become a better person, and an inspiration to others.