They have learned actually
Do you like it or not the overall number of social concervatives worldwide is bigger than the number of people supporting the mandatory manifestation of LGBT rights in any and every aspect of a product. Note - there is a significant difference between LGBT rights and "mandatory manifestation of them in every product".
The fact that some LGBT groups are extremely loud does not suddenly make them a majority. So from a business perspective Nintendo has learned and learned well and they have made their choice - stick with the majority of the audience (something Nintendo has been doing all the time).
As far as losing billions in a market, that is exactly what they have assessed here. They do not want to have half of the world closed to them because of including the LGBT option - off the top of my head that makes the game unsellable by law or social convention in most of the Middle East, Africa, Latin America, Russia, etc.
Is their choice morally right? That is a different story. Is it the right choice from a business perspective? Sure it is.