I think this sort of risk-reward-consequence will come with increased fidelity to gaming. Hopefully with more power in the hardware running this sort of stuff, more can be dedicated to AI to make the NPCs react more realistically. It's certainly true as gamers, we're all used to the 1-button press, no consequence insta-kill, but some moves towards making you hesitate have crept into games in the last few years.
One example is L.A. Noire (- for all it's faults) certainly made me hesitate when deciding who to send down for a crime. There was one Homicide case where a Husband (and father) looks good for the murder, but your bosses are pushing you to "pin" the crime on the other, secondary suspect because he's got priors as a paedophile, - but however much of a low life suspect number 2 is there doesn't seem to be much evidence that points to him being responsible for the death, even after I'd dragged both of them through the interrogation process.
When it came down to deciding who I actually fancied for the crime, it was one of the most difficult decisions I've made in a video game of late, and I certainly hesitated when picking between the suspects - I think this reaction came from the quality of the acting, and the visual representation of the suspects in this game - I've blogged about it here if anyone is interested in further reading; http://codename21blog.blogspot.co.uk/2011/06/game-update-lanoire-did-i-just-send.html
I'd be interested if anyone else has any other examples of when NPCs have been "humanised" to such a degree they've felt guilty about pulling the trigger...