Animals have parasites and diseases, so do plants, there are even bacteria that cann dissolve oil spills or plastic or what have you - why couldn't there be a disease living off magic - a magic item could be infected, losing power and speading the plague to other equipment it contacts, while a magic user would slowly lose his powers and contaminate all he works with or casts a spell at...
Many games draw moral lines in bold colors, where the real world is not so easy to categorize. Suppose that the player characters are faced with an overwhelming foe? Even unsavory allies such as orcish barbarians may be better than no allies at all. More disturbing, these allies may be honestly friendly to the PCs when all is done, overcoming barriers of race and religion. Will the PCs remain friendly with the bloodthirsty humanoid tribesmen when their mutual foes are defeated? Some would expect the tribes to betray them, but after the characters have honestly won their respect, even orcs may not be all bad.