There's certainly been a lot said on this topic, and I think we can all agree that an accept or decline pop up would have been the most simple and easy thing to avoid the mess that followed.
But I do have one other take on this that hadn't occurred to me before reading Bono's comments. I think that even without the accept/decline - Tim Apple could have presented this on stage at the event in a way that would have completely inoculated it.
Instead of having Bono do the whole "how can we get this out to half a billion people in 5 seconds... thing and having it be Bono focused with the little pre-rehearsed back and forth, Tim could have said something like - Because we've had a long and successful relationship with this band, and we value our customers long and faithful relationship with us, we wanted to try something new today. As a gift to our itunes users, we are going to be giving this amazing new album from U2 to you for free. The band has been compensated of course, because we are a company that is working to make sure musicians get paid for their art. So right now, we are going to send this out for free to all itunes users as a show of appreciation to you.
People would have been ok with this. The band would have been separated from the actual placing of the album on itunes.
They wouldn't go ultra-hyperbolic admonishing Apple, and giving them shit, they are loyal Apple customers and this would be nothing to the average user, and a cool thing for fans and semi-fans of the band. It was only fun to freak out on U2 because people love to knock celebrities off their pedestals.
Anyway, I also have seen a lot of comments on YouTube that younger people actually discovered the band through this, and found some songs they really loved, and searched out more stuff from the band. So in the end, it did have some success, but not nearly enough to outweigh the negative.
P.s. I say this about the Apple event, because I watched it, and even though Bono mentioned something about getting paid for it, I still came away with the impression that U2 was giving away their album for free through Apple. From the reaction, I believe 99% of everyone else thought this too.