Depends on when and how! If Viola tried to intervene after the overt abuse was already ongoing, there are two ways it could go: either she gets Isabelle out before Alec even knows what's happening (a la Nullverse) or he finds out what she's up to and kills her over it (a la my friend Ira's delectable fic A Family Portrait, which I will be linking below).

However, I've had plenty of AUs where Viola finds out while the abuse is still more covert - that is to say, while Isabelle is less than fourteen years old and Alec hasn't raped her yet. In those cases I think Viola might genuinely try to kill Alec, or else take Isabelle and run. Afterwards she'd try to be a better mother to Isabelle, but would still struggle to mend the gaping wound between them. As I always say, we live in the worst Viola timeline.