Yes, a Sabretooth would work fine, as would most other MOSFET H-bridge based motor controllers with PWM support.
You can write code that calibrates for two motors of different RPM/torque characteristics, yes. It will be slightly more complex than the one-motor-type version, though, especially if you want to compensate for things like varying inertia in the different motors.
My suggestion would be to buy two motors that are the same, and save the existing motor for another project.