It is difficult to keep carbon from entering into the combustion chamber when cleaning the exhaust port. Can a minute amount damage the cylinder walls?
yes.. I make sure the piston is up to level with the bottom of the port and vacuum while scraping. The other way is to gently blow air in though the plug while you do it.
When I have done it I have removed the cylinder and used a hardwood dowel shaped into a scraper to remove the carbon. Why risk scoring a piston when it only takes ten minutes to remove the cylinder?