It's because you're stealing. If your neighbor has a dog that he beats and neglects and you steal it you've still committed a crime. Yes, you did it for the right reason, and your neighbor was evil and wrong for what he did, but you still took something of his that doesn't belong to you. Same deal with monsters. Anytime you use the stealing skill to take something that is not yours, you will get flagged.
But by all means feel free to murder the earth ellemental and his citrine will be yous free and clear.
From my experience, any successful use of the stealing skill vs. a mobile results in the criminal timer.
