Warning her not to harm him is exactly what he needed to say to make Graendal feel like she was the hunter. If he had said "don't fight him because he'll probably kill you like the others, and you can't hurt him anyway because then I'LL kill you", she would have just fled Arad Doman altogether.

His words and instructions were carefully tailored. He even knew the exact bait to use to get her in the right frame of mind (knowledge, and a peek at Mesaana and Demandred). And he calculated her mood so well that he knew not to let her have TOO much faith in his favouritism (when she makes a coy remark, he rebukes her, and she recoils as if slapped). Because if she thought he favoured her, then she might have felt she could leave AD and still be forgiven.

In fact, we see in Moridin's manipulation of Graendal a foreshadowing of how she will be defeated. Graendal works on the premise of people having a conscious, and selfish motivations. She never considers that Moridin wants nothingness. As such, he is able to easily manipulate her, and Rand, once he takes on his dark, nihilistic persona, can easily destroy her. Graendal can only manipulate people she understands, and Dark Rand and Moridin were not acting within the realms of human reason.