I agree.
IRL, I am an atheist/agnostic. Default position is no god(s) exists unless you can meet a burden of proof. The burden of proof is very small. Inanimate objects can prove to me and other random people that they exist in a satisfactory manner. Paperweight on my desk? More proof for its existence than god(s).
In a fantasy world gods actually do exist. You can interact with them. They do stuff. Same with magic. In the fantasy setting it does exist, and so I have absolutely no problems working with it. My favored fantasy RPG character class is a paladin. Ironic for an atheist to play a paladin? Not really.
Some things you just need to accept to make the setting work.
Star Trek has its dilithium crystals. They have magical properties that are impossible in real life, but they are required to make the setting work. Dwarf Fortress has its mushroom based economy. If you get some mud on the ground it will sustain a complex economy forever, despite no nutrients being added in. There is absolutely no logical reason why it should make any sense, but it is required for the setting. Accept it and move on.
Same deal with gods and magic in a fantasy setting. They exist. They make the setting work.
Actually, that's why there is a big push behind that "Improved Farming" thing... but that's ignoring the forest for the tree.
There is good reason for what pilsu is saying - players embark in "evil" biomes for a reason - to face far more terrifying challenges to survival than in other biomes. "Evil" in this game is countered by its opposite "good", but "good" is largely absent in DF. That is, there is plenty of pillage and rape and murder, but little that demonstrates good, nor any real reason to pursue it. What happens in good biomes? You have fairies and unicorns and fluffy wamblers. How are they good? I dunno!
Likewise, demons exist, and actively lead goblin armies or pour forth from HFS. Gods or angels do not apparently exist.
Goblins are eeeeeeeeeevil, but are any races good? Well, humans are just plain boring neutral. Dwarves, at least under the control of the players, are generally more evil than even the demons themselves. It takes some serious stretch of the imagination to see what parts of the elven lifestyle could actually be seen as altruistic.
Hence, DF is a world that seems to have been built with a vestigal structure of good vs. evil, but really has a moral system that seems built around "violence vs. more violence".
This, however is getting away from the point.
We can assume that undead appear in evil biomes because of some innate power in an evil land - apparently, there is a force that reanimates the dead, and drives them to violence. This force, however, is only a stop-gap implimentation, and is not particularly well explained.
Regardless, we could, theoretically, be able to have a means of reducing the risk that the evil biome poses by trying to either prevent that energy from reaching a certain area (which would be something like a non-evil bubble in an evil biome), or counteracting the undeath effects by putting out some kind of energy field that would disrupt the process of animating the dead.
Of course, that's put into the vaguest of terms possible, because there really is no understanding of how, exactly, "evil" biomes work. They just are, and they are because they exist just to give players more challenges.