I don't think it's even meant to be ambiguous. Superman is screaming for him to stop and Zod outright says that he never will stop trying to kill, pretty much forcing Superman to stop him.
Yeah that's how it appeared to me as well. Obviously Zod could have easily
sliced that family in two with his heat vision, but he realized he was beaten and had no more purpose left with Krypton gone, and so he put Superman in a place where he had no choice but to kill him.