At the end of the day, I don't think trying to divorce Diana's costume from the American flag will work, for the simple reason that readers know it quite obviously is based on the American flag. Whatever the in-story justification, she's wearing the US flag; in her original incarnation, and in many others (such as the recent DVD), it was quite explicitly the US flag. She was created to be a patriotic superhero. Perez's story's acknowledgement that it was the US flag and justification of that is more workable in that sense.
If I created my own "Wonder Woman" patriotic hero, and she wore a red and white costume with her underwear covered in stylized maple leaves, and then tried in-story to say that she wasn't wearing the Canadian flag, it wouldn't fly.
If you could successfully divorce the costume from the flag in readers' minds, it would be a good idea, but I think it's a futile attempt.