That's why this decision (marred though it is by the game's limitations) is so fascinating.
Given that your small squad is the only one in a position to make a difference, and that no one else can make the decision for you, what's it gonna be? It's wonderful to see arguments in favor of short term "collateral damage" for long term benefit, or saying screw you to the "greater good" when innocent lives are at stake.
I agree with you Sausage, that thinking it through and "playing God" is unpleasant - in fact I'd say that only a real asshole could ever feel good about it - so, emotionally, I'm sympathetic to the point of view whereby you don't think about it too much, do the obvious thing, and save the most people; but deep down I have to agree with
Kaivokz. Spider-Man taught us that when no one else can make the decision, you have to man up and do what's right. To refuse consideration of the future implications, just because you don't want to be responsible for the immediate consequences, is simply selfish.