Three factors enter into how well you can see a medieval city from the air at night.
First, outdoor lighting is almost exclusively torches and oil/fat lamps (depending on the situation). These aren't very bright, compared to modern streetlights or yard lights. Second, due to cost, such lighting is likely to be as sparse as it can be, without too much inconvenience to the nobles and merchants (i.e. the slums will be very dark, the better parts of town merely quite dim).
Third is a matter of how well nourished your witch is -- many, if not most in medieval times were undernourished, if not flat out malnourished, and the latter, especially, will greatly affect night vision -- to the point where someone near starvation will be effectively blind after dusk. The same may be true even if your witch has enough calories in his/her diet -- if they aren't getting enough of certain nutrients (protein and vitamin A), they may find even a night lit by full moon still so dark it's very hazardous to fly at all after dark.
Also worthy of note is that most of the time, in most uses, outdoor lighting was applied only when needed. Torches wouldn't normally be kept burning all night, they'd be lit and doused as needed; if there was a torch in a holder outside the tavern door, it was probably cold and there for convenience in case of the need to greet a lord's carriage. Indoor light leaking out of windows won't contribute much, either, as shutters or curtains would likely be closed after dark except in the hottest weather.