Jon never would have wished it normally. But it was a stable time loop. He made a wish which would, much later, force him to travel back in time and make the very same wish, keeping the time loop going. And it also forced him to make the second wish:
"I wish that I would become Karyn's sister Megan."
Jon suddenly felt the weight of two breasts pushing out of his chest as he transformed into what he remembered as Karyn's older sister. The pocketbook that she was suddenly carrying on her shoulder contained a wallet and a student ID which showed that Jon's age hadn't changed at all--she was still 17, so from what she knew about Megan this must be about three years in the past.
Of course, since nobody else had heard the wish, Karyn (now about 14) wouldn't think Megan had just came into existence--she, and the Jon of this time, would remember Megan having always been around.
She still had the stone, but there was no way to reverse wishes. She had no choice but to live as Megan. She might try to tell Karyn, but there's no reason to think she'd be believed, at least not without using the stone. Would Karyn then be forced to pretend they didn't know about it to keep the time loop going? She had no way to tell.
Megan walked towards Karyn's house. Towards... home, for now.
