I do not sew over pins. I have computerized Bernina machines. I don't know if sewing over a pin can damage a machine.(?) (Maybe a question for your dealer to answer) But my concern has always been breaking a needle while sewing over pins. And thinking about a piece of the needle flying up and getting in my eye. Maybe I'm just being over caucious. :)
I guess this would be an individuals decision whether to or not to sew over needles.