3 options, the software option, the electronics option and the hardware option.
1. Go to the firmware. There you can configure the steps per mm of each axis (though I am at this point not sure if it is possible for the gantry).
2. Under each stepper motor driver there is a header with jumpers. Here you can configure microstepping. Make the 1.8 motor the default, and configure the 0.9 motor so it has 2x less steps (if the 1.8 motor has 1/4 steps, make the 0.9 motor 1/2 steps). This can also be combined with the 1st option.
3. Make the 0.9 motor a 1.8 motor. This is the easiest, though I understand that you are looking for an alternative.