Well I'm not familiar with that motor but most Kubota engines I've seen are built similarly. The water pump is probably driven by the fan belt but I don't know for sure. If it's belt driven it would make it hard, not impossible to turn over were it frozen. The oil pump and fuel cams should be driven via gears under a cover on the front of the engine. The only way to disable the oil pump would be to remove that cover and pull out a gear.
You could pull the fuel pump out of the equation by pulling the cover on the right side beneath the pump, unhooking the governor linkage, removing the fuel lines, and then unbolting and removing the pump.
It could still be the hydrostatic pump. The tractor rolling with the motor off only means the rear drive motor(s) are turning free. No way to really check that or remove it without splitting the whole machine though. Can you find an access cover somewhere around the flywheel? Check and see if anything is apparent in there. Also you might try pulling the starter and making sure that spins freely.
If it comes down to it the oil pan on my tractor was relatively painless to remove and the gasket came off easily. That'll let you inspect the main and rod bearings as well as the oil pump, liners, and piston skirts without too much hassle.