From Universal Mind
Killing 999 innocents to save 1000 is much closer to immoral than killing 1 to save 1000 because of the lack of certainty of the numbers. Also, you need to take into account the fact that we are killing and capturing terrorists like flies, and you need to consider that we are changing the political landscape to take the region out of the third world. The idea there is to create a much better future, one where people do not become suicide bombers.
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Taking away two Islamofascist governments and the power they could provide from the face of the Earth put a big dent in that plan. Taking them out of the third world is going to have a further positive effect.
Perhaps the reason we are capturing and killing terrorists like flies is because there are so many of them. It's as if the War on Terror hasn't had any effect at all, unless you count the NIE's statement that the number of terrorists is growing, despite all of the killing we're doing. It's almost as if more terrorists are created than we are destroying. Is it so far-fetched to think our actions are exacerbating terrorism rather than tamping it down?

Any action, no matter how vile, can be justified by arguing that things will get better in the future for the victims, and that will make it all worthwhile. The future will always be better than the present at some point, regardless of what atrocities take place, and such an justification takes advantage of that inevitability.

I'm not sure what 'plan' you're referring to when you say the war put a big dent in it. If the plan was for the cycle of murder and revenge to continue indefinitely, then it is certainly moving along as planned. If you are referring to terrorist plots to gain political power by inciting chaos, that's going along well, especially since the only secular dictatorship in the Mid-East is gone. What plan are you referring to?