Agreed, that's something I think generally works so well about TiTS: if there's something in game that you're not interested in or more importantly something that really puts you off (e.g. for me that would include mind control/alteration and anything with zero consent) you can avoid it without much trouble. Unless you lose some fights, I suppose (and lets face it, in this universe being quasi-raped is apparently more inconvenient than traumatic).
More directly on topic, I was enjoying the Atha stuff, even though it's side content it was a nice bit of universe building and was fun and light-hearted. The sudden left turn was a little disturbing but on the other hand I think you could make the argument that it's not something your character has a choice in, it's a separate side story and so the author can basically take it whatever they want. They seem to be telling a corruption type of story (thinking back, I think it is hinted at in earlier episodes), which while also not exactly my thing, is something a lot of people like.