I think the fact that there was a television crew there to begin with was something of a problem. A bunch of teenagers turned saving lives into a spectator sport to get rich/famous, basically. When something goes very wrong as a result of even slight negligence, to people who are hurt and afraid, that looks pretty irresponsible. However much of it was the producers fault, the heroes should never have agreed to let television producers manage and control the means in which they did their jobs.
Again, the general public was on the pro side. A few pockets probably weren’t, but the early protests against Bush’s actions were small, few, and got little media attention compared to all of the people rallying behind him. The number of people/characters arguing for each side isn’t what balances it, it’s the actual argument, and I’d contend that the actual arguments were fairly skewed in against registration. As you said, there were some grievous moral errors on the pro-registration side, and the anti-registration heroes had arguments a lot more convincing, in many ways, than “it’s dangerous not to.” There were both philosophical and practical problems with registration that I feel were addressed far more heavily than anything other than the practical advantages of registration, which seemed to be the only major talking point anyone on that side had. I agree that the debate part could have been handled a lot better, but I really don’t think showing faceless, nameless throwaway characters (or introducing characters entirely to make arguments within a specific storyline) spouting off rants about it would be the best way to fix it.
I think that does come out, several times, in the repeated offers to surrender and ask them to register before actual arrests. Otherwise, if they had reservations about arresting people who violated a law, they probably wouldn’t support that law.
They storyline is fundamentally about an ideological conflict within the superhero community, a climactic event other than a battle between themwouldn’t have made sense. Are you arguing for a more amicable ending, like in the “X vs. Y” comics of old, where the two heroes fought to a standstill until a new threat arrived for them to team up against? I feel like that’s been played out, for one thing, and it wouldn’t really be a workable solution, either; once Doctor Doom or whoever was defeated, the story would be right back where it started, with the heroes in conflict. I’m not saying the battle was well-executed (I wasn’t happy with the way Civil War turned out, either), but I think it was one of the few workable endings.