No, Apophi don't kill Pharaohs. They haven't since the ascension of the Mamano Lord. Nowadays, Apophi corrupt Pharaohs and turn them into sluts in order to rule over their lands. Usually, it ends up with both the Apophis and the Pharaoh married to the same man. It's entirely possible that this particular Pharaoh and this Apophis's mother belong to the same man's harem, and the Pharaoh helps raise the Apophis girl while her mother is busy ruling.