Honda Service center won't help you much. Even if they do, the quality of their work will be questionable. I always take my vehicle to Honda for mechanical work.
I would imagine that the small visible rust spot that you see is the tip of the iceberg. The damage will be much bigger in hidden spots.
Take your car to a good trusted body shop where someone can give you personalized service who will pay attention to the work.
I got my work done from a friend who owns a shop. He cares more about our relationship than the money he makes. He supervised the work himself and got the job done carefully. All rust was removed/sanded down. Patched where required and coated with rust inhibitor. After that in the hidden areas, they sprayed thick undercoating spray which itself has rust inhibitor. The visible parts got primer and paint. The key is to find all rust areas and treat them as best as you can.