I understand that your story was just a one-shot, but since you bought it to my attention, I thought I'd give you my 2 cents on it. To be honest, I've never been a fan of the angst "trend", mostly because it's so overused, and usually just gloomy for gloomy's sake, so to speak.
Even with your explanation, the entire story hinges on Simba and Nala being unable to see their son is still the same son they loved when he was younger, even though Kopa hasn't done anything to justify their hatred other than existing. If there were more steps between them going from loving Kopa to hating him, it would make Kopa's plight much more believable (especially if he did more in the story other than cry -- didn't he ever try to stick up for himself, try to act normal to convince others that there was nothing evil about him, or angrily lash out at his parents for their ignorant superstitions?).
For instance, if Kopa had developed a friendship with Asante prior to the time of this story (an idea which I have been trying to expand on in a WIP fanfic of my own), that would have given Simba and Nala more than enough reason to make the transition from mild apprehension to full-blown fear once his mane started coming in.
(Also, why would Kopa be thinking like a little kid if he is supposed to be 19 years old (at least near the end of the story)? :/)