That's an interesting take on it. The companions changed the course of civilization drastically by their actions on the ship Noah. Although they were not responsible for the events surrounding Palma, which I would think to have the largest impact on their civilization, the damage to Motavia thanks to losing the computer network was massive. Who knows how many lives were lost because Rolf landed the final blow on Mother Brain, rather than seeking some way to reprogram the computer?
If you think about it, Rolf and friends may have really "destroyed" two civilizations. After all, if they did wipe out the last of the Earthmen, that's another whole civilization and history lost. Even though they were corrupted, there's a degree of moral ambiguity to killing all of them.
It makes me wonder... would the Elsydeon cave be considered Heaven or Hell? On the one hand, it seems peaceful except for the ghost monsters. On the other, what soul wants to be stuck in a frozen cave for 1000 years?