Yeah, but that's ice-skating uphill. Superman literally says "mercy", doesn't lay a hand on Bats, and retreats. It's a really weird read to say he was supposed to all-in on threatening Bats. At that point, you're not just fighting the lines or delivery, but also the facts of the situation on their face... that's starting to become a tortured interpretation and ice-skating uphill.
On face value it's a weak threat, but it's meant to be. Contrast that against Batman beaten down in the rain. There, Superman's voice is raised, they've already fought, and he talks about taking Batman's life not just his cowl, and there's immediacy ("Stay down [now]!" versus "Don't go to it [sometime in the distant future].") and intensity to it... but even there he's declaring his reluctance to fight in that clearly more heightened situation... so it makes sense in a more sedate one Supes isn't good a delivering threats.