The whole intent of this dark scheme (which I would never expect to have enacted of course) is as a deterrent. Who would want to go through the rest of their lives as a completely impotent (both sexually and intellectually) man. The lobotomy also prevents any other terrorist schemes to come from that mind. If he kept full use of his intelligence, I would expect he would use it to strike back still. It isn't so much meant to be a lifelong torture for him as a symbol for those that remain.

Mind you, I'm not really this cruel, I just needed to give the reptillian part a little leash after the attacks; and that's what it came up with.