I know I've done this quest successfully, but it was a long time ago, and I don't remember exactly what had to be done to identify the leaf. The things I can think of to try are to click on the crafting table (which it sounds like you've tried), click on the leaf in the inventory, or click on the spy to see if it's a self-interaction. As for your spy not knowing how to make sleeping draught, that shouldn't make any difference. The game wouldn't have let you take on the quest if your spy wasn't at a high enough level, and I don't think that quest requires the spy to be at a particular level anyway.
