In considering big moral questions, it sometimes help to reduce them to small scale analogies that are closer to home.
Let's say that members of a gang invaded your home on 11 September and killed some of your family members, some of the gang members also dying in the process. Subsequently the gang threatens further violence against you.
Later you find that members of the gang, possibly including those who planned the first attack, are sheltering in another house up the street. The home owner does nothing to help bring the gang members to justice, and does not kick them out into the street where you might be able to do so yourself. So the question is, would you be justified in breaking into his home to get them yourself?
Maybe, you may say. But how about if you were likely to kill some of his children in the process?
Hmm, more difficult, huh? So the real question is, should the US attack al-Qaeda members in Pakistan against the wishes of the Pakistani government? And can they do this without "collateral damage", i.e. risking the killing of innocent Pakistanis in the process? Just one of the difficult questions President Obama will have to grapple with.