You are correct, the M106 S# command controls the fan output. Here's the thing though, the Ramps board is a true 4 axis board, all that needs to be done is reassign the extruder axis from E to one PEP5 supports such as B or C and set the steps per mm to run either a stepper tied to a MA3 or a DAC. I do realize you haven't tested this setup, all i'm asking is in theory would this work possibly with the gcode PEP5 would output? Here is a picture of the Ramps board and pinout.
This is the pinout for 3D printer applications, but the firmware has been modified already for CO2 laser use using on/off and PWM.
I'm just testing the waters to see what will work or may have the capabilities of working. I may possibly run a crowdfunding campaign on Kickstarter in the fall, and would like to keep this as reasonably priced as possible when it comes to the hardware and electronics. The cost difference of your software just to feed an Arduino gcode is a fraction of Mach 3 doing the equivalent thing, not to mention arduino hardware is much more affordable as well.