I don't know if this discussion is over yet, but anyhow my 2 cents on Shinn's intentions:

I am 110% sure he meant to kill both Kira & Athrun. While there might have been hesitation inside him, I am quite sure he is not the kind of guy who does something in a half-assed way. Once he sets his mind on something, he does it. That's just the way he is. I mean if he had any suspicions that Athrun/Meyrin were still alive, why would he break down like he did with Luna?

It will be funny once he notices that both of his kills were void though. [img]i/expressions/face-icon-small-tongue.gif[/img]