Aww fuck, so the game screwed him over hard this time. I think the Kusora route's done for, but I could actually see her forgiving him since she's messed up in a lot of ways.
That said, to the people calling this guy an idiot etc - have you even read this series? We know:
1) If he doesn't clear the mission before time runs out, he dies. This mission clearly stated that the target is the short-haired girl.
2) Whenever options pop up, that is the correct route. Every action taken to avoid that choice results in a bad end.
3) If both bad end routes are chosen, a third "true" one can pop up.
Obviously it sucks to betray Kusora and this is very likely to bite him back if there's no 3rd option, but the game gave him zero choice. He's acting perfectly logically.