Recently, the part in Urth of the New Sun where Severian kills the female torturer has been brought up as evidence that Severian is still far from being Christ, or even the perfect Christian.
That's a fine and correct statement, but I think there is a more important thematic reason for it. If you look at the mythology invoked in The Book of the New Sun, from "Eschatology and Genesis" with the evil Jalee to the Uappes tribe of Brazil in the Botanical Gardens, you see that the evil deities are overwhemlmingly female. Over and over, you see scheming females, whose only redemptive quality is their ability to birth children (thus the importance of Dorcas being Severian's grandmother and being one of the few positive female figures). Severian overcomes these females, and even the threat of emasculation by reasserting a manly rule - it's not a distinctly Christian figure, but a powerful male figure who eliminated the unnecessarily cruel female element of the torturers. We all know that Ymar will abolish women from the guild, probably because of his treatment at the hands of the woman that Severian killed. That act in the past liberates Ymar to rid the guild of women, and frees Severian in the future from having to deal with them in his safe tower of masculine "might makes right but follow the pecking order" guild. Note that there really isn't that much duplicitousness of scheming in the tower at the time of Severian - they just follow orders. I see that strike as a final assertion of the masculine future that Severian wants to be raised in. And I think he only saves Agia because of his presentiments - he knows that she will save him from Vodalus and certain death in Citadel of the Autarch, because he's gone through the cycle before, so everything seems familiar to him.
Marc Aramini