You could always use wooden shingles as your roofing material (with a waterproof layer and insulation underneath).
What is a natural solution for insulating a roof, other than soil?
Katee mentioned wool and clay slip/straw. Others include cork, woodfibre, hemp, hemp/lime, flax, woodwool and cellulose. You could also consider thatch made from reed or straw as this insulates as well as forms the roof itself.
Oh, and you could recycle/reuse artificial/synthetic forms of insulation if you're ok with having that kind of stuff in your house.
Why do you have to dig a trench, fill it with gravel, and then build the foundation up out of that?