4 pin fans aren't backwards compatable with 3 pin headers but 3 pin fans ARE backwards compatable with 4 pin headers.

The motherboard doesn't care if there's something plugged into the processor fan header or not. I just unplugged mine with the system running with no ill effect.

Try it.

EDIT: Wait, are you saying that the fan is getting its power from the 4 pin molex connector on the motherboard?