On the broader question, religious circumcision involves an irreconcilable clash of rights: the right of parents to practice their religion versus the right of children to bodily integrity. We resolve this contradiction differently for boys and girls. That's not rational but it's the way it is, and likely to remain for the foreseeable future.
On the religious basis of female circumcision: this is found in the haddith not the Quran, which does not even mention male circumcision. The fact is that genital cutting is a tribal tradition of Western Semitic peoples predating the Abrahamic religions and its real origins have nothing to do with God's will or immortal souls.