Is the Internet security battle lost?

According to this New York Times article, researchers at Stanford University vote in favor of starting all over, redesigning the Internet. I wonder if that is the way to go? At the same time, they suggest an evolutionary approach:

“They argue that their new strategy is intended to allow new ideas to emerge in an evolutionary fashion, making it possible to move data traffic seamlessly to a new networking world.”

The Internet has indeed been evolutionary, how can one prevent ending up in the same mess once again?