Betraying America

You'll recall Marvel Comics' Civil War that I mentioned in a previous post.
The war is over, and one side has definitely won.
Quick recap:
The United States Government decided, after massive deaths at a school in Stamford, Connecticut, that all superheroes would register with the government. This meant every hero would:
1. Reveal his or her secret identity to the authorities,
2. Accept training from the proper authorities, and
3. Hunt down heroes who don't register as enemies of America.
The heroes of the universe split into two groups. One group, led by Tony Stark, better known as Iron Man, agrees to join the government. The other group, however, is led my Steve Rogers, better known as Captain America, which surprised...well...everyone. Captain America is supposed to represent America, but in this case, he makes himself a traitor to the country he loves (he did it once before where he resigned and became "The Captain") because he truly believes that what the government is asking is violating civil rights. Remember: Steve Rogers is about representing the ideals of America, not its government.
The two groups battle each other over the course of a few weeks.
Spider-Man reveals his true identity to the world...then changes sides when he sees the plan the government has for the heroes who don't change: Prison 42 (think Gitmo, but in a different dimension).
The heroes on the Registration side clone Thor (the Norse God), and, due to faulty wiring, he kills one of the heroes.
Villains are recruited to help the government capture heroes who have decided not to register.
In the end, the heroes have a huge fight that ends when Captain America surrenders. He realizes the damage the heroes are causing, so he orders his side to give up...and they do.
There are even farther reaching reprecussions as well.
Spider-Man's family is attacked, Captain America is assassinated while walking from court, Tony Stark turns out to be a war profiteer, and now, to be a hero, everyone must reveal real names.
What I am fascinated by is not the war itself, but the message Marvel Comics seems to be sending with it. Let's look at the facts:
Captain America, the very essence of America given human form, is killed. Is Marvel saying that America is doomed?
The guy put in charge of the government office to oversee the heroes (and who led the winning side of the war) was able to make millions off the destruction of a city and the death of innocents. Iron Man even betrayed his friends to do so. So, the people in charge of the war are, in fact, evil in a way. Is this a commentary on our current political setup?
The Registration Act itself is a thinly-veiled take on the Patriot Act (with the reasoning for the act an allegory for 9/11).
The other issue is how Marvel maintained that both sides were equally right, but neglected to look at the heroes on both sides.
The most popular heroes in the Marvel Universe were on the side of those against registration.
This included Captain America, Daredevil, Spider-Man (once he realized why it was wrong), Wolverine, and the Punisher.
The heroes on the other side, outside of Iron Man and Mr. Fantastic, were not the most popular. Is this saying that while some heroes disagree, the ones we like the most will always be on the side we (meaning the general public) like?
I also find it fascinating that the Punisher, who many consider a ruthless killer, may take up the mantle of Captain America as seen here. Is this saying that to defend America, we need to be ruthless in our aggression?
Should these comics be considered treasonous? They make the representatives of America (Captain America, above all) into criminals, and they attack this "beloved" act that protects our citizens, or so we have been told.
If you get a chance to pick them up, do so, and let me know what you think.
Then again, what do I know? Iron Man is at my front door, and I need to register or go to jail. I could be wrong.