I too reread the comic before the movie, and once again after. I think the movie, in many ways, was superior to the comic. With the movie, I was emotionally invested in the characters. In the comic, the characters were all angry caricatures of themselves, with the exception of Peter, who is fine, and Tony, who is now The Ethical Savior of the Marvel Universe. The movie did not provide any clear answer as to who was right, but the comic is pretty clearly trying to say that Tony and his side are right.
Wow, really? I came away from the comic thinking they played Tony off as some kind of suddenly-insane Nazi (which annoyed me). I still think he was right, but I feel like the writers (Mark Millar especially) really didn’t like him and went out of their way to make him unlikable.
I also thought that the whole event started to drag after awhile and it was just people fighting for no reason anymore. This might have been the point, but it still got a bit drawn-out near the end.
I did appreciate that the movie was more ambiguous about who was right, though.