Hi Andre,
If the EasyDriver you are referring to is the SparkFun EasyDriver, then the A3967 IC on the board has built in protection diodes so that its internal transistors are not damaged by back emf.
You are right to worry about the motors affecting the Netduino. I was using a similar circuit with a 9V battery supply (6 x AA 1.5V) for my buggy and had to give up powering both from the same supply because the Netduino kept re-booting when the motors turned.
I was never aware of any damage to the Netduino - I think it was just brown outs, or maybe noise that was enough to trigger a reset..
If you are worried that the driver board will feed current back to the 12V supply, then add a rectifier diode in the positive line between the battery and the driver so it can only take current - that should protect the Netduino from high voltages.
(Note that the EasyDriver circuit does not have any protection for its own logic supply, so I don't think they are expecting any problems like this. However they do have a 30V tolerant input.)
You might also add a similar diode to the Netduino supply input and add a big capacitor after the diode so that short brown outs are less likely to reset the Netduino.
Let us know how you get on.
Have Fun - Paul