What army could have stood up to 1999AD if they were already dead. Lavos' strike was so random that nobody had time to prepare. Also, Porre possibly has the elements on their side.
And another thing, Crono and co probably did not need to fight 1000s of monsters in the Black Omen to get to Queen Zeal. Remember, monsters and leveling up is a game play aspect, not plot or canonish.