I added fans to the backs of my computer monitors to allow them to run cooler and hopefully extend their lifespan. I used computer CPU fans similar to yours that have the 4 wire connections including the PWM input. To lower the noise and be able to control the fan speed I built a simple little box that takes in 12V from a AC->DC wall type power module and then outputs that to four fan connectors on the back of the box. Internally I designed a very simple circuit that runs off 12V and uses two 555 timer chips to produce a 22KHz requency waveform and then uses a pot on the second 555 timer chip to create a PWM signal to drive the four fans.
I'll post a picture of the schematic later so you could use the same design if you wish.
You can easily use a MOSFET if the Fan specifies a weak internal pull-up and a 2N7000 fits a 12V low current application.
Whether you should worry about the fan supplying more than officially specified, is another thing. If you have shorted the pin to ground for your measurement and 0.68mA came out, that's so incredibly well within the reach of a 2N7000 that you shouldn't worry about the FET too much. You're welcome to worry about the Fan itself, if that helps you in any way, but a quick test with an arbitrary PWM signal will show if it is broken, or just built different to (EDIT:) the official prescribed spec.
All in all, I say, go for it. If you are really doubtful, you can limit some FET damage by adding a resistor in the drain path, like so:
simulate this circuit – Schematic created using CircuitLab
The 2N7000 has an absolute worst case drain-source resistance of 13.5Ohm (the one Fairchild makes, at least) and I expect in your use-case that it will not exceed 3Ohm even when hot.
(EDIT2:
Sunday made my maths go wobbly, changed the voltage drop and the conclusion to it in the following block:)
So at the very worst the resistor and the FET will share the risk, normally the resistor will catch the brunt of it. At 5mA maximum the resistor will only waste 0.05V, which is negligible, you can even increase it to 20 or 30 ohm and it should still be interpreted as low. In the worst kind of failure (PWM shorted to 12V in the fan) the 10Ohm will effectively limit the current through the FET to about 1A (if the FET also is at least 2 ohm then), which is an acceptable very short-term limit. 30Ohm would probably keep the FET fully safe until the resistor itself burns through.
9999 out of 10000 times the resistor is completely redundant and pointless. But it is an option if it helps you sleep better (2 cents for good sleep, I call a steal)
Best Answer
4 pins fans are brush-less motors, the same as low noise fans. Those fans have electronics inside and they may not tolerate higher voltage. DC motor with no electronics works fine with higher voltage PWM.