I have a few theories on this, they wouldn't have introduced her if there was no reason. I think one of the possible answers is that she became bens wife and got pregnant and died. that would kinda make sense with ben trying to solve the fertility problems and that he took alex instead of killing her, also he statement made to juliet by Harper i think, that " you look just like her" this has been speculated that she was refering to bens mum but could have been about Annie.
Or she could have been sarificed during the purge of course
Or ben could have been in love with her, And thatshe knew about the purge and Alex and couldn't cope and left the island spurring ben on to become the leader of the others.
It has been annoying me for ages aswell