The main problem I've always had with that saying is what if you're saving the wrong people? That's not to say you shouldn't still kill them but it would seem like you're killing them for the wrong reasons. Then again does it really matter why you're killing to begin with? In the end you're still making a permanent change in the world however insignificant it might be overall. That's not to say all deaths are insignificant, merely that statistically speaking most murders don't change the world on a global political, social, economical, or other scale.
Who's to say this should be painted in one light or another either. It's not a purely good or evil action ever, and even which side is stronger is both highly conditional and extremely subjective. I also wonder how many times a given person has been or can be saved? What if you're killing one of those thousand that is supposed to be saved? All coming back to the end of it all remains the fact that it shouldn't matter how or why you kill. The point being that you're going to do it one way or another, justification is frivolous and if you need it to be at peace then what are you doing killing in the first place?
Of course all of this may just be me out on my own, share your thoughts on murder in general in the comments. Would you do it, why you would do it, how you'd do it, how you'd cope if you needed to or reasons why you wouldn't. How it changes you, or the world, just any thought in relation to the subject.