How do I reduce the Counter EMF?
Since it is a small motor and you are thinking of using an L293D you could use the chip to brake the motor before reversing it. If you disable the pair of half-bridges that is driving the motor it will free-wheel (coast). If you drive both inputs low (or high) and keep the outputs enabled it will dynamically brake the motor through the H-bridge. This will cause a similar surge to when it starts up. If you either measure RPM (with an encoder or whatever) or wait a sufficient time for the motor to slow to near stop then you can apply reverse voltage without getting the double current startup surge you would otherwise get from 'plugging' the motor. Since the bridge is absorbing the surge from stopping and immediately afterward a surge from starting you should evaluate the capabilities and make sure it will be okay.

You could also use the remaining drivers in that chip to switch a dynamic braking resistor across the motor (which is easier on the H-bridge and the motor), but directly shorting it will stop the motor faster.