I do not disinfect my eggs. I incubate in cartons, tilting the cartons, and even flipping the cartons (so that the right end of the carton now becomes the left end of the carton), AND moving the middle eggs in a carton to the ends, and moving the end eggs to the middle... AND every few days, I rotate the eggs in their egg cups. I'm a bit OCD about this, but it helps me to ensure that all eggs rotate through any warm/cool spots in the bator, and that the eggs get turned well.
If an egg is dirty, I don't put it in the bator. But, I hatch from my own flock, and it's easy to pick and choose which eggs to incubate, and even increase the bedding so there are very few skid marks on the hatching eggs.