Then he thought to himself. Jon and Karyn had a good chance of messing up the stone's wishes anyway. He mumbled a few magic words to himself and touched the fake stone. Ahh... that was interesting, he thought as he got glimpses of some alternate possibilities.
A lot of things Jon would do with the fake stone would cause him problems, true. But as the intruder thought about it, he realized that many of those wishes would be very unwise even if Jon actually had the stone he thought he had. He didn't need to replace the stone--he could just let Jon make those wishes and things would be messed up anyway!
He pocketed the fake and dropped the real stone, right where it had been a minute ago.
The next morning, Jon woke up to find the stone on his dresser, right where he had left it. It looked for all the world like it was unchanged... because it was.