Killing you was one of the things he was supposed to accomplish while infiltrating the Big Shell. You'd been a scientist at Shadow Moses, similar to Otacon except that you'd continued your work on Metal Gear. What he found out instead was that you were charming and in a few conversations he had to admit to himself that he enjoyed your company and was now debating whether or not to let you live instead of following through with the task. Though he scolded himself for the thought "Damnit"