I guess instead of saying "Well, you didn't declare that you were doing nonlethal damage, so he's dead now," the thing to do would be to gently confirm "...And you're going for lethal damage here?"

You know the PC probably isn't intending to murder the guy, and a major characterization faux pas like that shouldn't happen by accident, so if you see it coming, head it off to make sure the player understands what their character is doing. Part of the DM's responsibility is helping the players visualize the scene accurately and this sort of thing is part of that. An alignment shift is a consequence of an act of will, not a procedural error.

So go easy on the player. It was mostly your fault.