I dunno. Jean fixing Emma didn't do much for their relationship the first time she did it.
Having Jean do it again, and in a younger, less experienced, and ostensibly non-Phoenix powered state would probably only further drive a wedge between the two.
Emma can be hard to get a bead on, but I disagree that she hasn't had a stance on the 05. I wouldn't says she got hostile but of Scott's side she was the most vocal about sending them back. During BotA Emma was the one who alerted the other X-Men and the Brotherhood to where the 05 were so they could come and grab them. And I think her telling the Cuckoos to leave Jean alone was largely a self-preservation angle on their behalf. She knows that as her "daughters" the Cuckoos would be mightily tempted to mess with Jean, and Emma knows better than most just how hazardous that can be to your health.
But since Emma's the only fully trained psychic around (and Rachel is not in the picture) she pretty much is the only person qualified to give Jean some direction on how to use her powers, since up to this point Jean's understanding of her own abilities has largely been trial and error. I think there is potential for an Emma and Jean mentor/student relationship to bear interesting fruit, just so long as it's not a repeat of the BotA encounter...