I think there's definitely a strong predisposition to read things that way

Yes, absolutely. I agree with you that the story undermines the usual OTP readings where of course these two would wind up together, the "Big Love" ideal that permeates WNG - to my reading the story clearly implies that without this experience, there would be no (sexual) relationship. But at the same time I still believe that the political aspect of their relationship is only possible on the basis of the personal - the way I read it, the one strand in all of this that holds steady while sexuality and identity and circumstances are being twisted around is their personal friendship.