In my mind, this is how I would bury the log home:
Logs on top of some sort of foundation, round stones (perimieter drain rock) outside of the logs, sheet of plywood holding the stones back, felt or tarpaper, a few layers of poly or some other waterproofing sheet, then the dirt. Not sure exactly about how to waterproof the roof, probably the same thing only without the stones. I don't want them to behave like little wedges up there.
I had thought to use solid logs across the top as well. I have driven over many log bridges on long abandoned logging roads and I think that they would well support a thick layer of dirt and some horses or an occasional tractor.
A couple other random thoughts.
At this stage I have not yet priced logs. Maybe concrete is cheaper?
Being so near to this clay bottomed pond may require pilings?
Since I need some excavation done for both this house and in general around the farm, I had thought to buy a used excavator to dig my own holes, and then to manouver the logs during construction. After the house is done and the other bits of digging and dredging are done around here, the excavator would be sold.
I have not yet considered a building permit.
I have considered sewage and electricity.