I’ve kept the Eradication in my campaign, but I view it in much the same way as some of the reasons for the Cleansing Wars.
The races chosen were divided into two camps, those with a very large population/fast breeders and those with advanced psionic or magical traditions. The key to the Cleansing Wars was to provide life magic to Rajaat and prevent anyone from organizing enough power to stop the spells Rajaat would use to return the world to the Blue Age.
The Eradication occurred when the druids finally realized what was happening to the land (the Spirit of Athas simply losing touch with areas that were defiled before eventually losing much of it’s “consciousness” and having to be buttressed by druids becoming Spirits of the Land) and organizing a resistance. As long as they existed in a loose scattering of druid circles they weren’t a threat. Once they started communicating and organizing, they could have stopped the SMs.
Once they were decimated and driven into exile, they stopped being a threat. They aren’t actively hunted by the SMs anymore unless they try to organize. Many of the SMs actually use them to help tend the fields, the forests, the groves of trees of life. The SMs have come a long way in understanding what defiling does, but aren’t willing to give up the power and abilities it provides. Druids can help balance that damage, as long as they remember their place. If they forget, the SMs will squash them.
Clerics are concerned about restoring the world (with their chosen element in dominance of course), in exchange for the power they are granted by the elementals. As long as they don’t try to organize a rebellion against the SMs, they are useful in keeping the masses working towards helping the planet recover. If they stop being useful, the SMs will squash them. If they try to promote their element over the SMs, the SMs will squash them. If they interfere overtly with the templars, the SMs will squash them.