I'm positive Necron has no connection with the Tree. Just assuming it rethought its entire reason to exist after Garland died sounds a lot like making excuses to me.

I think he's some ancient being that has always held his radical beliefs, including the belief that life itself wants to be erased. When Kuja tries to destroy the Crystal, Necron believes that his views are confirmed and tries to blow it all up. Zidane and friends fight him and show enough strength to convince Necron that life isn't ready to be erased yet. He retreats back to wherever he was before, waiting until life wants to be destroyed.