Actually, that was Garland. Kuja wanted to take control of Alexander with the Invincible but he didn't know Garland was in the Invincible, it was Garland that used the Invincible to level Alexandria, Kuja's current intention was just getting control of Alexander and I'm sure he would have used Alexander to destroy Alexandria shortly after, but Garland interceded and took the glory from the field.The only kingdom he destroyed on his own and easily (despite the legendary Alexander) was Alexandria.