I don't know, Moffat seems to be intending lots of things. A lot of people were saying that they thought the Doctor was getting darker without the narrative noticing, and then bam, the narrative was all up in that. Maaaaaybe Moffat is all over this kind of creepy best friends' daughter thing. I just don't trust him to be oblivious anymore.

Either way, I totally understand your squick. I've only recently been able to ship Doctor/companion at all, and Doctor/companion's kid is pushing it a bit far for me.