That’s a nice idea. We’re working on a remote control pioreactor that we’d like to be able to use with schools. We were contemplating using a syringe for inoculation (mainly for visual impact), but your dual-purpose waste pump could simplify things.
The ‘Maker Drive’ that you linked to boasts ‘Reverse Polarity Protection’. I’m no expert, but I’m wondering if it deliberately avoids reversing the motor. I was also thinking that a stackable HAT solution might be nice. Possibly this Adafruit DC & Stepper Motor HAT for Raspberry Pi - Mini Kit (also available from the Pi Hut). I think you’d also need a stacking header (Adafruit/Pi Hut) and standoffs (Adafruit/Pi Hut).