Salmonella have two ways of contaminating eggs: They either infect the egg the time it develops in the hen, or they latch onto the shell and come in contact with the inside when the shell is broken.
While the only thing to get rid of germs in the first case is heat, you can prevent salmonella from spoiling your eggs in the latter case.
Just put your eggs in a bowl and gently pour boiling water over them. Turn them around to ensure every part of the shell gets in contact with the water for at least a couple of seconds, then take them out and process them as usual.
Also, you can greatly reduce the risk of buying salmonella-infected eggs from sick livestock by choosing organic producers that raise chicken free range under proper sanitary conditions and who care about animal ethics.