Frankly I didn't know the audio was real at the time. I guess they could of rerecorded it word for word if they wanted to, however it's no more manipulative than if they'd shown footage of the planes crashing into the towers or people jumping from the floors before they collapsed. If anything it humanized the events, by giving it a voice Vs reveling in the visual spectacle. How else would you have had them set the film up exactly?
Re: Zero Dark, it was sombre but I think the audio in the beginning is emotional manipulation. Everything following that opening audio can be justified by the suffering of those victims and questioning anything is equated basically with questioning the suffering of those victims. I don't know if it was intended but it works very well I think. In addition, it seemed to me to glorify and humanize the SEALS as basically a bunch of nice guys doing a rough work.