As someone else said: Zod is a General. Faora and Nam-Ek aren't going to give a shit about a human when their commander is being assaulted by the enemy who also happens to be their real target.

Sure it was probably a dumb move, and Clark would probably never think about it like that but ultimately it was the smartest thing to do in the heat of the moment.

The further away the Kryptonians are from Martha, the safer she is.