The trouble is that mining methane ice is very risky, as it is close to the temperature of sublimation, and the entire methane ice field could have a chain reaction, resulting in an immense release of methane all at once. This would be bad.
One suggestion was that it would be robotically mined in an artificial Carbon Dioxide atmosphere. As it was removed, it would be replaced with supercooled water that would quickly turn to ice when sprayed into a gap where methane ice had been. This would also help to structurally support the mined area.
IIRC earth's original atmosphere was mostly methane. It took billions of years for it to dissolve and settle to the ocean floors resulting in the unique atmosphere we have now.
The methane ice layers are not a new descovery. You are correct that it has been left alone for fear of disrupting such a fragile, ancient and life supporting ecosystem.
yitbos