The way I see it: Tobias was little more than a pest to Hannibal but instead of killing Tobias himself, Hannibal made him useful by sending Will after him. In doing so, he could accomplish multiple objectives at once: 1. ridding himself of Tobias, 2. bringing out the dark, violent side of Will, and 3. further testing Will to see if he was worthy of Hannibal's "friendship." (I'm sure jealousy/possessiveness played a role too but I don't think Hannibal was aware of it yet. He still thought he was in control of everything; he didn't recognize that Will was changing him until later.)

The most interesting part of this episode to me is how Hannibal reacted when he thought Will was dead (and later, when he realized Will was still alive). Up until that moment, he had always played with people for his own amusement/to satisfy his own curiosity but was never really emotionally invested in any of it. I'm not sure he realized how much he wanted Will to survive until he walked into his office at the end of Fromage. The relief on Hannibal's face was genuine and fascinating. I doubt he had ever felt anything like that before.