What are you talking about? It is still the same +12v, gnd, gnd, +5V as the 4 pin molex. Sure you might have to lop off the connector and either add your own or attach the fan wires directly to the PSU wires or twist up the bare fan wires and poke them into the floppy connector then tape it all up good but there is no reason you cannot do that.
Just make sure to only use the fan's red and black wires.
Actually, why not pull a power connector from a dead/crappy 3.5" floppy drive and solder that to your fan wires?
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