Why did the Waknuk people shoot Sophie?

This question is a bit misleading.  It makes it seem like the Waknuk people stood Sophie up and had her executed.  That's not quite how it happened.  Earlier in the novel, Sophie escapes the Waknuk society by going to the Fringes.  Sophie must escape because she has six toes.  That makes her a Deviant.  The Waknuks are basically okay with Sophie escaping and removing her DNA from the Waknuk gene pool; however, that is not the case when David and his fellow telepaths escape.  The Waknuk people, including David's father, begin hunting David down.  David and his group then get captured by the Fringes, which ends up leading the Waknuks to the Fringes.  A battle soon follows and "the spider-man" shoots Joseph Strorm in the chest.  Sophie is standing next to the spider-man at this point.  

Suddenly he stiffened. His bow came up like a flash, bent to its full. He loosed. The shaft took my father in the left of his chest.

He and Sophie then try to quickly flee the battle.  While fleeing, both Sophie and the spider-man are shot and killed.  

Sophie struggled to her feet and ran on by herself. An arrow pierced right through her upper arm, but she held on, with it lodged there. Then another took her in the back of the neck. She dropped in mid-stride, and her body slid along in the dust...

Perhaps they were natural casualties of the battle, or perhaps the Waknuks intentionally targeted Sophie and the spider-man for killing Joseph Strorm.  Either way, the Waknuk people don't view Sophie and the spider-man as human.  They are Deviants and deserve death.