The more I think about it, a better counter question for you is this:
Do you, or do you not, think that what went on at Abu Grhaib, alleged abuse at Guantanamo, et.al,-- if all proven true- are acceptable things that were "necessary"? If so, then it seems Americans are sharply divided on what sort of values we want our country to espouse and what the concept of "freedom" represents in terms of our laws and legal system and then I don't know if that rift can be closed because it is so vast. If you think the above abuses were unacceptable, then why do you care that the ACLU and other agencies are not also pursuing al qaida and abuses in other countries? That isn't their job. I was under the impression that the ACLU is a domestic agency that concerns itself with watchdog activities in our own country to prevent abuse of government power. The analogy I'm making is that this is like chastising the Medford, Oregon police force for not pursuing lawbreakers in Miami, Florida.
It's about upholding expected standards- and most Americans hold the US at a high standard. Everyone around the world already knows that Al-qaida, who are largely individuals identifying with no nation- has no standards at all. Eliminating their threat will come from military actions and cultural isolation that can only result from Middle Eastern countries coming up to speed with human rights- and if we don't set an admirable standard to present to them as a contrast to their own, WHO WILL DO IT?