Agreed. That said, it's hard to justify why your PC would keep her around unless he subscribes to her nonsense.Ember is good not because her dialogue is good, she is good because the other companions have a lot of unique responses to her mildly retarded lectures which can be of really high quality.
I mean, you can say that it's just because she's useful (something which you are allowed to explicitly acknowledge in dialogue), but that's far from a satisfying reason.
I don't immerse that much, my party is an alignment clusterfuck as I only choose by gameplay and writing quality.
There is something quite interesting however if you want a roleplay reason to keep her around, Wenduag is scared shitless of her because she senses something is off. You could keep her around as any lawfull character in a "I want your Jesus shenanigans where I can see and control them, and not have a second crusade start in my back" fashion.
Also another thing on why her writing is good, her character lets the other ones talk about stuff that is not exactly their gimmick. Nenio is so shit because she always keeps her SCIENCE! gimmick up. It makes her onedimensional. If the other characters are talking about something not directly readable from the first paragraph of their backstory it is probably because Ember said something stupid.
It is like how in real Pen&Paper the best roleplayers are the ones who stop the party from just being a bunch of charades following a simple script to acting like they are a real group.