After some further reading, instead of disconnecting the fan wires, I used the method of slipping some folded paper into the vents to stop the fan. The machine is completely silent now, as expected. It feels a tiny bit warmer to the touch, but it's difficult to tell. No other ill affects observed.
you should either disconnect the cable, or use software to kill the fan (google) - by the sounds of it your fan motor is still going, which will kill the motor, and still use power and make heat. its trivial to disconnect or use software.
posting this on my eeepc, love it