Pure has different definitions and connotations along with it. Pure is often associated with goodness but I remember back in DBZ, it was said that a Super Saiyan arises when they are pure of heart. In Vegeta's case at the time, he was considered pure evil.
In the case of Sasuke, Sasuke is pure in the sense that he does not act out of what he thinks is good or evil, rather purely off of what he wants for himself and honoring what he thinks to be the wishes of his family. Sasuke is pure in the sense that he has no care of evil or goodness, he just wants to do what he feels is best and acts upon that. Whether it's best for himself, for Itachi, the Uchiha clan or even the village, in the sense where he considers he should be Hokage so that he can prevent the village from having a case of Madara again, or the scenario of what happened with his brother, where someone has to make a greater sacrifice.
You shouldn't look at it so one-dimensionally. When Kishi says Sasuke is pure, he's pure. It's just in a different connotation.
