THE BASIC POINT:
Even though the Kopa story doesn't completely change the morals of SP's story, it most certainly does take away from them by affecting their base crucially. You can't just throw a murder over innocence and expect that the morals don't crucially change.
As in there's a fine line between punishing someone for just loving a person and being a threat, and punsihing someone for the murder of your child. And there's a fine line between punishing innocent people for being associated with another innocent person, and punishing innocent people for being associated with a child murderer.
There are also those who vision Kopa not murdered but just disappeared in one way or another, which is a little bit better for the moral matters - but unfortunately the Zira-killed-Kopa has been accepted by FAR the most truthful story.
But there's one more thing. While the Kopa-disappeared version doesn't necessarely mess up the morals regarding Zira & company's exile, it does greatly affect the way the film's life lessons are seen. I mean, think about it: Simba and Nala have their first born child disappeared, so they let their second child run around with no appropriate babysitter watching over her, the mother is completely care-free about the new child, the father dreams only of his own father and any dark event leads to a reference to Mufasa and never to Kopa. And just generally a lost, dear child was never spoken of with so much as half a word in all those years. Those things are one more reason why both but especally the murder version is so NOT what really happened. Because such event/character-reaction combo is NOT what Disney does with their family films. It would be unrealistic and highly inappropriate.
// The Lion King, Simba and Kopa belong to The Walt Disney Company.
DISCLAIMER: I don't own the pictures used in this art but this is non-profit fan art for educational purposes only. No copyright infringement intended.