While this will work in most cases, it's not good practice (sp: practise??). What you are doing by using the difference between outputs of two supplies is sourcing current from the 12v supply and relying on the 5v supply to sink that current.

In the case that the 5v supply is sourcing a lot of current relative to the fan current to other devices, you'll probably get away with it since the other devices will sink the current rather than the power supply. There then becomes the issue of how well the 5v supply will regulate in this situation.