Adding the ability to modify frequency is easy in firmware.
But: It will not help if your laser (power supply) is not capable of pulsed operation.
Most DC gas lasers are CW (Continous Wave) lasers and not pulsed (like the more expensive RF (Radio Frequency) lasers in Epilog, Trotec and Universal laser systems).
If the PWM is used to modulate the laser power via the analog input of the power supply, changing the PWM has most likely no effect (apart from bad PWM to power linearity if the frequency is too high or too low).
If the laser power supply is capable of quickly switching the laser on and off, frequency modifications make sense. In this case the PWM signal has to be routed to the laser ON input.
I am not sure if switching the laser ON input quickly (at 5 to 10khz) kan damage power supplies that are not prepared for this, and I also do not know if would give improvements in peak power or beam quality.
We would need to do some measurements.