Personally, I think after this arc ends we shouldn't see Nova/Jupiter interact with the Sparkle family for a while. Not to kill her off or cancel her character, but to help develop her. Jupiter, from what we know, wasn't that great socially. Nova was just a child. This new pony should have the chance to go out into the world and find out who SHE is, not who her family have made her to be. And the only way she can do this is to be away from those who she's be relying on for so long.
And sure, in time bring her back. I would love to see the new Mare that Nova/Jupiter will become. And sure, maybe don't shut her out completely. I wouldn't mind seeing her out in the world every now again. All I really want to see is Nova or Jupiter, or whoever this new pony, will become on her own.