My idea of trying to compensate for the vibration by changing the shape of the outside of the wheel so that the surface that touches the blade is stable, was stupid. Because bearings last much longer and require less maintenance if they don't vibrate. Your idea to actually reduce the vibration rather than merely compensate for it, is of course much better.
I knew an electrician who worked on a lot of motors and pumps. He had learned how to extend their lifetimes from weeks or months to over 30 years, from repair shops, motor manufacturers, and experiment.
E.g., he learned to mount motors and pumps together without detectable vibration: The motor axis the pump axis should exactly align, to eliminate sideways pressure on the shafts and bearings. And there should also be no along-axis pressure between the coupled shafts.
An absence of sideways pressure isn't perfectly possible in a skate sharpener. Because When you sharpen, you also place pressure that is at a almost a right angle to the shaft. But it still makes sense to minimize vibration, and align things as well as you can.
P.S. He also learned other things that helped: in terms of maintenance, voltage (and the best ways of compensating for voltage drops), power conditioning, load balancing, making electrical connections that were more corrosion resistant; and using over-rated heavy duty motors, wires, transformers, and impeller blades. He also learned to correctly select overload breakers and fuses (motor manufacturers use a different breaker rating system from most electrical appliances, so electricians who only read the National Electric Code learn wrong). He specified plumbing changes to reduce pump water pressure. He learned that a wiring diagram provided by a motor control circuit provider omitted a key component.