We'll probably have to play that out, since Loki isn't a bloodthirsty monster that wants to just kill people for fun most of the time. More it's a question of what's expedient and will make the chances of success the best. If they don't have a good way of kidnapping the chief programmer, I think he'd definitely be of the opinion that killing her is the much smarter option. Since if they are trying to keep this covert, having a hostage will make getting out way, way trickier.

Tony's heart attacks are like candy to Loki. ;)