16 pin SOIC is hardly large enough to worry about. I think that getting the fan speed dealt with in hardware would be preferable to getting hijack to do PWM speed control. Sure, there would need to be some coding done, but it should be trivial compared to implementing a user-tweakable PWM control.

A (probably stupid) question - Are there suitable fans with tach output? I'd hate for everyone to go this route and be unable to get fans that woulf fit. I'm sure there are, but we should check