Nope, won't hurt the steppers at all, nor a properly designed driver. Not sure what the ones coming out of China are like, but in general, they shunt anything over their rated voltage to ground, or short it across the windings.
I doubt you can spin the handwheels fast enough to generate enough voltage and power to harm the drivers. But the handwheels won't turn easily. They "notch", as steppers do, especially if under power. As was said above, the vibration of the off-axis handle weight can cause a problem, mostly in the form of mashed fingers and possibly broken bones. A little machine may "whack" you, a big machine has the power of the stepper, plus the "umph" of inertia. Broken bones *can* result. After all, if it can snap off a 3/4" endmill, it'll make a meal of the dinky bones in your hand.
If I HAD to turn them by hand, I'd put a fairly well balanced handwheel on the, minus the handle, and stick the shank of a hex wrench in the hole to spin them by hand when necessary.
But honestly, jogging in the CNC software is usually fast, easy, and easily different feed rates are easily selectable.
The only use I could see in manually jogging via handwheels is touching off a tool. And that I'd even do via the CNC controls. Run it close by eye, jog careful until it squeaks or cuts. Either way, you've probably got enough stock to clean up without worrying about a .005 margin of error on the rough cuts.