I think you can turn off Story Progression from the options menu, at least that is what I have heard.
But, as for what happened...I have not personally had this happen but I think they just move into a random house in the neighborhood. So, look around for a bit and in the families bin too. Once you find her you can evict her and then merge her back with the family that she came from.
Edit: Apperently that is not quite what happens. It seems that the sim vanishes entirely. But, there is a chance that they will come back. If that happens, make friends with them again and just do the above if you can find where they are living...