Just as hostages can come to bond with their captors, so you end up liking GLADOS - the female-voiced computer in Portal, the Best Game Ever Made (TM). Guilt for killing her is prolonged because you have to do it a piece at a time. While she talks to you. Don't worry though, it's OK - she forgives you at the end via the medium of song. Er... time to play a different game, we reckon.
Above: You didn't really get emotionally attached to this thing, did you?
What have Goombas ever really done to you? If you stand in front of them and they crash into you, you die, but then that's true of buses and you don't go around stamping on them, do you? These days the small brown critters might charge at you when they see you, but surely that's because they're standing up for their rights after two decades of repression. And if that wasn't enough to get your guilt gland fizzing, look at the score you get for killing them. 100 points. They're the gaming equivalent of the £1.99 whole chicken. Has life really become so discounted?
Above: Look, just stop jumping on them already! Pick on someone your own size