I don't like that too, but that is the way games are nowadays. Interactivity is limited to shooting baddies.
What are you talking about?! Games are getting more and more open all the time! Deus Ex/DX:IW? NOLF1/2? System Shock 1/2? All of those games offer a measure of choice in who you kill or rather how you play the game. It's certainly more open than it's ever been. What did we have in the past? Doom, Quake? There was hardly even a plot, leave alone a consideration of the merits of leaving characters x, y and z alive.