In that at first, the battle was going to be a draw, but Joss Whedon convinced the writers and editors that a side had to lose, someone had to die (Millar actually credits Joss for this idea). It wasn't going to be Stark because they already had plans for him re: Secret Invasion, and with regards to cap, it was either death or be depowered (lose the Super Soldier serum). Brubaker was offered those two options and took that one.

I guess Captain America as Nomad wouldn't have flown again? He still would have been persecuted.