DC Motor pwm control and flyback diode question
During pwm off period, the motor current freewheels through diode.
  Won't the motor experience a braking torque then. Is it desirable for
  efficiently controlling the motor?


Firstly, Any PWM signal frequency should have a time period that is many times shorter than the physical response of the motor due to it's mechanical inertia.

And, as Brian Drummond reminded me, the diode will only conduct due to the initial back emf from the inductance of the motor. After this has settled-down, if the motor is continuing to free-wheel in the same direction, the diode won't remain forward biased. However, the motor free-wheeling will generate a voltage and so, it might be advisable to put a diode across the BJT - anode to ground - to prevent any excessive motor free-wheeling from reverse biasing the BJT to any great extent.