In other words, you should really be comparing to the children who would have died from terrorist actions if we hadn't launched those wars. It's like calling doctors murderers for providing a vaccine that kills one in a million, but prevents a disease that, left unchecked, would kill one in a thousand [2].
In either case, which people die are real and knowable as individuals, but which people are saved are hypothetical and statistical. You choose the best course of action from the alternatives available, but sometimes it's not possible to choose a course of action that saves everyone.
In other words, choosing the greatest good for the greatest number may result in some disquieting sacrifices -- we wish the world didn't work that way, but we must base decisions and actions on the way the world actually works, not the way we wish it worked.
[1] "A few" and "a lot" are relative terms.
[2] The scenarios aren't exactly comparable, because there are presumably plenty of well-designed studies which rigorously establish the number of children who would have died in the disease scenario.
The number of children who would have died in terrorist attacks in a different foreign policy scenario is much more difficult to estimate, and much dependent on your assumptions of human behavior: A hawkish viewpoint might say that if we hadn't counter-attacked with the war in Afghanistan and our drone activities, the terrorists would have been able to build strength and launch more major attacks; a doveish viewpoint might say that our military activities in the Middle East are a big reason the terrorists hate us, and if we don't attack them, they won't attack us.
We can observe that, having launched the wars and drones, the US has not suffered another attack of the same magnitude as 9/11 in the decade-plus since; the hawkish scenario is supported, or at least not ruled out, by the evidence. The doveish scenario is also not ruled out by the evidence, but we can't know for sure what would have happened on the road not taken.
Presidents have to make world-altering decisions on the basis of equivocal evidence and their best guesses of the future interactions of humans with wildly different cultures and sometimes-irrational thought processes. This is why I stick to math and science.