Mathiasgranger and Vanir, the former being one of my favorite authors (along with yourself, of course), and the latter whose works I have just begun to explore, covered the main hypotheses I wished to state.
Yes, Hermione could make a horcrux, the poison could do its despicable job, and The Brotherhood could make her a new body; one that still had the ability to reproduce, as you are so fond of writing her and Harry of doing. But you said yourself that it wouldn't be that easy because it's called "The BROTHERhood"? Well, that's a fairly foolish bit of hairsplitting if I've ever read any. You've been writing that the BH is beginning to go through a time of renewal; inducting its first female member might be a good part of that process. Besides, do you really expect that with as open-minded as you have written some of its higher-echelon members as being, that they have existed for over six millenia without one woman joining them?
More to the point, who said Hermione would even need to be inducted into the BH. It might be a poor example, but Riddle certainly showed that being a BH member is not a requirement for the production of horcruxes.
There is the possibility of Hermione becoming a vampire, another pseudo-immortality that the BH created for friends and lovers of its members, but that still leaves the problem of the potion destroying her body from within.
Perhaps the Invincible Mind of Granger (TM) might be turned to finding a way to save herself, such as hitting the myths, as Vanir suggested.
And then there is the easiest solution of all: Time-Turner.
So, apart from the horrible thing that happened, but that you can easily write your way out of with so many reviewers clamoring for you to do so, this was another phenomenal chapter to another phenomenal story.
I eagerly await the next.
There's a reason why there are no sisters. A vampire would overcome the basic problem, but as Harry will point out, vampires aren't very cuddly