actually GT you bring up a really good point, and that scene is one that i forgot entirely while writing my previous post. i will need to rethink this. off the top of my head maybe he saw what she was doing as an attack on how well he does his job... and by letting her get away she outsmarted him or outplayed him (even if only in his head). like all the lies she told him in the previous scene about the mountain climbing enraged him, feeling insulted she would try to put that past him. and truthfully, he gains nothing by letting her live considering he's been concocting his own agenda, she's just a liability that would be a loose random factor. but that's a weak assumption I'll give you that, just popped in my head.
I'll add more detail to try to convince you about my point. By killing her, all he stands to do is cast doubt on himself in the allies' eyes. He wants them to believe he intended to help them as soon as he got wind of Operation Kino, but he kills their double agent for no good reason. If Allied forces did a basic investigation of her death they would know that and put blame on him which could compromise the benefits he wants as a new American citizen. No, he compromises his new allegiances by killing her so the reason has to lie on a personality deficiency within him that goes against his full professional character. It has to rest on his prejudices in some manner.
