The battery will absorb a not insignificant amount of braking current. If you supply the MCU from a psu circuit with high enough max input voltage, then it is quite possible that's all you need. You cannot easily use overvoltage clamping diodes or TVSes since you don't have a low impedance reference handy where to shunt the overvoltage. The battery won't do because that will always exhibit the voltage of your regeneration...
Depending on the size of your motors you might need braking resistors to keep the voltage in check. But then you also need a way to activate the resistors which creates more complications... Easiest solution: design the MCU psu with high enough max input voltage that you won't hit it in normal operation. Possibly you will want to look into some kind of emergency crowbar if there is a real risk of significant surges.