To clarify, you had the bucket partially filled to give more weight/traction while pulling something? If that is the case, I don't see how that would directly in itself affect the main shaft in the drivetrain. Even if, with the added traction, you were abusing the tractor trying to pull something, the cause and effect through the drivetrain would have created problems before it reached the back of the engine. It sounds like, to me, that there were problems with the mainshaft/clutch already, and this was the straw that broke the camels back. It may be expensive, but I believe that it was inevitable.
In the future, though, loading the front like that could cause you problems with the front axle. These tractors are strong, but not indestructible. Nothing is.
2000 hrs on a B7100 really isn't much- there are many out there with much more than that- but that depends heavily on its life and how it was treated for those 2000 hrs.