I'm thinking of cutting down a stepper motor's shaft and flattening one side (using a dremel). Would the vibrations ruin the motor's guts?
I would be more concerned about heat build up then vibration. Work slow and let the work cool down frequently.
Lefty
Good point, thanks for the input 
I'd also tape any holes and the base of the shaft to protect against filings.
Rob
Try and clamp the shaft in a vice when you work on it so you do not put strain on the bearings.