Whole tournament was just Zeno testing the virtue of the winner by putting in a hidden rule about the wish needing to be done in good faith. He never really wanted to erase the universes but had no problem doing so if they showed more signs of greed or evil than empathy when given a moment of god worthy power.
If the wish was made for selfish reasons, the winning universe gets erased as punishment since greed was picked over being righteous. Rest of the universes would have stayed erased as the somber legacy of the bad wish.
If the wish was made in good faith, it would have proved the virtue of the winner since personal fortunes were sacrificed in favor of the well-being of everyone else. Rest of the universes get revived as the virtuous legacy of the good wish.