Yeah that's what kills it for many people.
I saw the scene differently. While it was bad dialogue, the scene made it seem like Batman, I guess for the first time, saw Superman as a human being (as much as he can be considered) with a family. He had a mother and someone that loved him enough to plead for his life. This also ties into the beginning flash back of Bruce Wayne's parents murder. Not just the uttering of the name, but of Batman realizing that he was now about to do the same thing to Superman as the person who murdered his parents did to him. Batman has essentially become that which he loathes and fights against. Which is why him not branding Luthor was so important as he had been inspired not to take life (in an indirect way) by Superman or Superman's sacrifice. One could see the film as Batman's redemption. This also ties with Superman being a light for humanity/role model because if he can change someone as stubborn as Batman then there's hope for humanity.
The movie reviewer, Chris Stuckman, did a rewrite about this scene (in which he got a lot of hate, even rape and death threats about) which hammered the point home much better. Maybe I like the rewrite because it's so close to what I thought about that scene so I guess I'm biased.