Yup, I've successfully incubated eggs that have been filthy with poo and with bad staining to the shell, after I've washed them off. I dunk them in a hot solution of dilute bleach, give them a gentle scrub to free off any muck, dunk them again and give them a swirl around for maybe 10-20 seconds, then rinse them thoroughly under hot running water. If the water is hotter than teh inside of the egg, it causes any dirt that is in the pores of the egg to expand and be forced out the way. If you use cold water, the contents of the egg will contract and actually suck the dirt further in to the shell.
Most people recommend water just slightly warmer than 99F, to make sure no heat damage is done to the egg. Personally I use water quite a bit hotter than that, as logically it takes way longer than 20 seconds for heat to transfer from the outside of an egg to the middle. But anything just over 99F will be fine...