Interesting. The molex mod in question treats the 5V line as ground, so current leaves the 12V rail and enters the 5V one. Power supplies expect to supply current on all the rails, and not recieve any.
Most of them seem to shrug off the unusual case, but there are theories knocking about that it decreases their lifespan. Your post supports this theory.
More usefully, go for 6V instead. 12V -> fan 1 -> fan 2 -> ground, the fans in series. As long as you have two similar fans they'll take about half the voltage each. The power supply will be quite happy with this. If you have an odd number of fans, you either go for an intricate arrangement of fans or run one of them through a resistor in fan controller fashion.