PWM of Diaphragm pump
Raising the frequency will not help you. Even at 100 Hz, the mechanical inertia of the motor will make it run smoothly. The only difference will probably be slightly more heat being generated, as the power transistor is switching ON/OFF more frequently.

Duty cycle modulation seems quite doable. The only slight problem could be that the load on the motor is not constant - at the max excursion of the membrane, probably the pressure on the motor is higher. So, at low duty cycle, the motor might refuse to turn, while still consuming energy. You can probably avoid that with a minimum duty cycle.