The resistor only protects the motor so that the maximum allowed current through the motor is not exceeded. When the motor accelerates and gains speed, the current drops, and so does the voltage across the resistor. You can increase the value of the resistor to protect agains "over-voltage", but then you are limiting the available torque you can get.
Resistor really is a bad solution, but if you need a fast solution to protect your motor, use it while you find a better solution.
EDIT: The speed of the motor is directly proportional to the voltage and is limited by the mechanical construction. If your motor can handle the speed it gains at 16V, then there is no problem. Exceeding current rating is more dangerous because current through the motor creates heat and can burn the motor. Using a resistor limits the max torque you can get.