The Queen wanted to use Atlan to deal with her enemies. If he became a lot stronger, then he could be the one to kill off her enemies for her.
By letting him live and grow up, then the Queen was basically investing in him.
It would be a win-win situation for both of them. Atlan would be ridding the world of powerful Canzers, and the Queen would be getting rid of her enemies.
Atlan had no choice but to accept her words. After all, the alternative would lead to his death—literally.
'So begone, human. I will not tell a soul about your powers.'
The Queen turned around and spread her wings wide. With nothing else to do, she wanted to return to her kingdom and spread the good news to her people. They would surely want a banquet now that the King and the Princess had been avenged of their deaths.
But just as she was about to take off, Atlan spoke out to her.
'Wait!'