Looking at the vishay datasheet for 1N4001 diode, this is what I see:
The maximum reverse voltage that the diode is going to see, is 12V. That would be when the motor is running, the mosfet Vds is as small as you can make it, and the ground is good. The maximum reverse voltage for the diode is 50V, or 35 V RMS ( which as far as I can tell is more or less the same thing ), so you are good there.
When the mosfet interrupts the flow of current though the motor, the maximum circulating current through the diode starts at a maximum value of whatever the load current was, and falls from that value back towards zero. The diode current is not going to be more than the load current.
Looking at the datasheet, the peak forward current for the diode is around 30 to 50 amps depending on the duration - in the order of a few milliseconds. If your load was 2 ohms, you'd be looking at a maximum motor current around 6 A ? That would mean a peak diode current of less than 6 amps, for less than a millisecond. It would appear that is not going to overload the diode.
The diode also has an average forward rectified current of 1 amp. Depending on the duty cycle of your PWM and the inductance of the motor, you might come close to this. You'd have to have 6 amps ( peak ) flowing through the diode for the equivalent of 1/6 of your total duty cycle, to create a forward current ( and diode heating load ), as large as 1 amp.
If you know the inductance L of the motor, and you assume that when the mosfet turns off, the +ve terminal of the motor falls to say -0.8 volts relative to ground, enough to turn the diode fully "on", then you can estimate dI/dt, and therefore estimate how long the diode current event lasts.