Its not like the voltage rating of the stepper motor means the isolation on the coils breaks down at that voltage or something, it is related to the power rating of the motor (you can put as much DC current thru the motor that develops 3V across the internal resistance and it should barely not burn).
In fact higher voltages are commonly used to get the current in the coils going faster - they are inductors right? - for high speed operation, as long as you don't exceed the power rating and back off on the voltage to 3V / limit the current when the max rated current is reached it will be perfectly fine.
Normally you think in terms of current not voltage when driving stepper motors...