I definitely would not try amonia on my wood floors!!! That is one smell I would not want permeating the wood. Has the urine actually soaking into thewood? If so, you may want that one spot refinished to get the odor out. We recently had that done. that area was resanded and refinished and it really helped with the smell that was already trapped in the wood.
You may want to consider crating your dog or buying a child safety gate and leaving your dog in the kitchen while you are out. This will help you with future accidents...Good luck!