There are certainly bearings in a water pump - no-one is arguing with you there.
However, the XJ/MJ with the 242ci six doesn't mount the fan clutch to the water pump (like everyone else does,) the fan clutch and fan run on an idler pully under the A/C compressor, and on that same bracket. That's why losing the fan clutch on an XJ won't necessarily kill the water pump - because the fan assembly would go unbalanced and end up killing the idler (and maybe dinging up the AC compressor clutch as well.)
They couldn't mount the fan to the water pump if they put in an e-fan - because there wouldn't be room. So, they mounted the fan off centre and added the secondary.
That's where everyone else is coming from - the fan clutch and fan aren't mounted to the water pump (like everyone is used to.)