You always defeat Lavos before he's done any real damage, no matter what time you defeat him in. If you were to defeat him after he's done damage, than what's the point of defeating him? The only difference in defeating him in 12,000 as opposed to 1999 is the amount of life he's sucked from the planet, but he does that so slowly it probably doesnt make much of a difference. The only time defeating Lavos would be worthless is after he destroys the planet, but that's impossible anyway.