Wait... Why would he make his sister make the wish? That's the absolute most surefire way for something to get fucked up. I'm guessing she would wish for her brother to always be happy, and for things to always stay the way they are, long before she would wish to be cured. Perhaps it's the reason she's feeling a bit better. Not cured, but not going to get worse sort of situation.
He seriously had one job. Hold a damn stone and wish for her to be cured. How did he screw that up?
Maybe, I'm over thinking it. Maybe the "Miracle" granted by the stone has some sort of caveat, or just isn't as powerful as folks think. Not much of a miracle then, but I guess we'll see.