The transistors you show can easily be change to Mosfet's with little circuit change. The Mosfet's drawn less current from the µP is their main benefit.
For not staying with the transistor schematic:
I would move R3 from the emitter of Q2 to the collector of Q2, and add a 250 ohm in series with the brake signal. This change will allow the circuit to work if the brake signal is 5V.
The BRAKE signal an ON signal would come from the µP. However if both the BRAKE and ON are high at the same time you would have a short condition from the 9V through Q3 through Q1 to gnd.
Question, do you need three conditions (ON, Freewheel, BRAKE) or only two (ON BRAKE)?