What I'm trying to get across is that you can't say that not shooting the girl and letting those thousands of people die is automatically the best option like steerpike suggests.
I didn't say it was the "best" option. There is no good option in the hypothetical. But not shooting the little girl is the least evil option (in fact, it is not evil, whereas shooting her is an evil act (and people could argue, I suppose, how evil on the scale of evilness). People may differ on whether they consider that "best" or not.