There is just one question in Crisis Core about Super Nova and it is an optional "side quest"
...so? Super Nova destroying the solar system still makes absolutely no sense according to the plot.

Even the one million laser attack of your precious Xemnas or his heart stealing attack.
There's two main differences though:

1. Xemnas' attacks don't break any plot rules
2. These two particular attacks that you've chosen are essentially unavoidable which the game itself forces upon to you to say "LOOK! THIS IS WHAT ACTUALLY HAPPENS!".


And of course in the Final Battle Sephiroth has a set pattern of attacks. I have never said anything against that. It is simply the truth.
Making him...not so challenging.