Betraying Fawn... No... More like Fawn, being Fawn.
She leaves after you force her to be more Violent on you while doing Bondage Play, and she absolutely does what is asked... the Upper-Ark scene is basically a choice on whether you want to have a more Serious relationship with Fawn.
And No it is not Optional Fawn's route goes there eventually, this is After Cassie, rescue operation so it will be deep into the game by then.