Anyway, I don't think the game pushes you to kill him. I did his mission before Virmire and everyone wanted Shepard to calm him down except Ashley who just wants to kill him. If you kill him, everyone except Ashley says they wish he listened. The options for killing him come out of nowhere too I feel like. If you kill him or signal Ashley to kill him Shepard makes no effort to calm him down and then if Ashley kills him on her own Shepard doesn't even get a chance to calm him down.
Moral of the story is, Ashely is a bitch. Does Kaidan have a better story than her in ME3? I'm really contemplating killing her on my NG+ file before I carry it over to ME2. The only thing that makes me want to keep her alive is that she gets hot in ME3.